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    Thread: 2001 Mk4 Jetta Auto (01m) to Manual (02j) swap notes

    1. Junior Member
      Join Date
      Mar 10th, 2009
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      South Bend, IN
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      2001 Jetta VR6, Wolfsburg 1.8T, 2004 Durango, 1990 Miata 3.0V6, 1966 AH Sprite
      05-19-2012 10:32 AM #1
      OK, I fixed my ailing 01M automatic problems on my 2001 VR6 by swaping to the manual 5-speed. The posts by Alphasenior, nosborn94, coolAirVw, swozniac4201, boertje, and many others on this and other forums were a fantastic help, and without them I would probably not have attempted the project at all. Unfortunately the down side of so much information is that it was difficult to keep things straight at times. In any case, thanks to everyone. It is running great now under the Automatic ECU and with the CEL on. The TCU still installed, but everything appears to be working as I had expected. If you don’t need to have the CEL off it is possible to stop here.

      Now it is time to give back a little. My hope with this post is that someday I may be able to help by making it easier to discriminate between the Diesel and the Gasoline swap, as well as the differences between a full conversion and one where you were going to run under the Automatic ECU. Yeah, I know, maybe it’s being picky, but it would have made life easier for me and it was what I spent most of my time on. On the other hand it made for lots of interesting reading.

      Anyway, here are a few things that I thought would be helpful to speed up the next person’s conversion and hopefully avoid some problems. I’m still looking at doing a full conversion by swapping the ECU for a manual unit, but that is in the future.

      Essential Elements:
      1. Swap trans and shifter per other threads.
      2. Install Clutch pedal and support bracket.
      3. Rewire 175 relay socket for 53 relay to provide clutch/starter interlock and backup lights.
      4. Connect backup light switch.
      5. Cut Yellow/Blue wire at the ECU that is also in the harness being modified under the dash and used for the backup lights.
      The details are more than covered elsewhere multiple times and, reading others experiences are of value to understand your vehicle’s differences and possible workarounds. Any additional wiring changes seem to be only required if you are going for a full conversion and installing a manual ECU. Otherwise you have a functioning conversion at this point and it is really not that difficult.

      Wiring: Be sure to check the wiring diagram for your vehicle.
      1. What I observed is that the wire colors are generally (but not always) correct in the other posts. Please use caution.
      2. The terminal numbers for the under dash wiring were correct for me, and probably will be for you, but knowing the numbers made things easy to trace on the diagram so check to be sure. See comments below.
      3. ECU wiring is different between automatic and manual, gasoline and diesel. Some terminals are assigned differently on the ECU.
      4. The diesel ECU’s can be recoded to manual, the Gasoline cannot.
      5. Check into your Immobilizer level before you commit to making ECU swaps. Past 2001 it appears to become more difficult to make a complete conversion. Read http://wiki.ross-tech.com/wiki/index.php/Immobilizer for more details.
      6. I left the TCU (transmission control unit) in place and connected. When I disconnected it the ASR light came on. ASR appears to be working with it plugged in.
      7. There is some throttle flair on shifts. This may be a programming difference in the response of the Auto ECU as compared to the manual ECU.
      8. The seat belt warning no longer works.
      9. Cruise works fine but only the brake pedal cancels it. I tried a couple of workaround’s for the clutch but they did not work.
      10. I did not have to do any wiring on the instrument cluster to get VSS to work. I just plugged it in to the old wiring harness. Actually I put the automatic sensor on the top of the manual gear adapter in the diff housing.
      11. Axles from the VR6 will fit the 5 speed manual trans.
      12. Backup light wiring and clutch starter interlock is like in the other threads.

      Brake Pedal: I had read somewhere that it was possible to only trade the pedal in the assembly and not the whole bracket to save some time and effort. This should work if your assemblies are compatible with each other. I spent an entire evening working on this with no success before I found the problem. It was totally my fault, and after I found it, it was embarrassing, but I wanted to help clarify things just the same.

      The photo below makes it painfully obvious why it won’t work in all cases, but I didn’t happen to look at the two from the side until hours later under the dash wondering what was wrong. The top lever is from my 2001 GLS, the bottom one supposedly is from a 2001 GTI. I really don’t think so, but not sure. The problem is the location of the pivot bolt on the left.



      Since the same steps are required to change either the pedal only or the entire frame assembly, I would take out the pedal first and check to see if it is possible to just swap it out before I removed the frame. It may be possible to save quite a bit of work. Even less work on the Mk IV is to just leave the Automatic brake pedal and use it like many have done (myself included at this point).

      Removing/releasing the brake pedal: The push rod that goes from pedal from the master cylinder is retained to the pedal assembly by a spherical end that is snapped into a plastic clip shown below. Whether you are going to change just the pedal or the whole assembly the clip will need to be released. Before you start it is advisable to hold the push rod into the master cylinder before you start. This is really easy to do if you look at the brake pedal frame assembly and the pushrod next the firewall. I pushed down the brake pedal with vacuum still available so that it would collapse more and put a screwdriver handle into a hole in the side of the frame to hold a large white piece depressed. It is not so apparent why to do this until you try it without. I didn’t get a photo of this but it should be obvious if you just take a look when doing the process.

      The photo below shows the broken clip in the pedal assembly I received, but it illustrates the clip that needs to be depressed on the bottom right (red circle) to disassemble the parts. On a good part there is a finger on each side. I made a tool like what is shown in the Bentley, but a moderately large flat screwdriver (3/8 wide blade?) worked equally well, maybe even better. What I did was to locate the tip of the screwdriver at the clip, pulled on the brake pedal while prying the clip fingers back by twisting/prying each side alternatively until the pedal pops free. Then pull it down and out.



      Clutch line clips: I struggled with inserting the retaining clip on the master cylinder end for quite a while until I noticed that the clip inserts from the fender side and not from the front. If I had looked closer before I installed the master cylinder I am sure I would have picked up on it right away, but I did not see any mention of it in any of the write-ups and after it is mounted to the firewall it is not easy to see. Even thought I don’t have a picture, I thought I would make a note of it to help others. Look at the master cylinder before installing it and you should be fine.
      By the way, the dealer only shows one clip for the assembly in their break down but there are three total used; one at each end of the line and one on the bleeder screw. They also call it something else but I seem to have lost the bag. The o-rings are called a “Washer”(p/n 02F-141-143-A).

      Clutch Bleeder Screw: My bleeder screw was fairly rusty. I should have done a better job of inspecting/prepping this part before installing everything, but didn’t. I was concerned that if I just tried to loosen it in place I would crack the plastic slave cylinder. The way the slave is made it is not intended for the clip to be easily removed with the slave the installed on the transmission. It might be possible to push out the clip from the bottom but I could not reach that very easily at this point. But, a little careful work with an 1/8 inch drill bit can make a recess that you can work the clip out from the top with a small pick or screw driver. It is not real easy to see in the photos below (sorry, but I was not able to get a good picture but you can get the idea), but the drilled area is just to the right of the clip and is only about .060 deep, which is just enough to let you get something under the clip and pry it out. Now you can pull it out to the workbench and clamp it to get the screw loosened. The picture also shows the power steering line routing I used. A little bending made it fit fine.



      Engine support: OK, not that original since I got the idea from another post somewhere, but improved on it a bit. Since I had the VR6 project, and some work on a 1.8T coming up I went a little further, but it turned out to be really simple. Some scrap 2x4s and a piece of threaded rod, nuts, washers, and some hooks welded onto the end and then, there it is. I put two boards flat to support he load and provide a wider surface for the threaded rod to go through. You may want to use a different configuration or use a heavier cross piece to support the threaded rod, but I found this configuration to work well for me. To fit different engines just re-position the top boards and screw them to the crosspiece so that they wont move around. Drill holes as required for the threaded rod above the engine hoist loops for your engine.



      I did put a shim (Blue Circle) under the front ends of the sidepieces and drilled short recesses (Red circle) for the bolt heads on the fenders to help hold it into position and cut notches out for the rubber bumpers that the hood rests on when closed.





      The location to drill can easily be found but fitting the boards and pressing down on them. You can then see where the bolts touch. I also sculpted out a little on the bottom edge away from the headlights to better fit the curve of the fender

      One note for use, the boards do flex under load and that lowers the engine about the correct amount to remove the transmission. I put a floor jack under my engine and lowered the engine to gradually put tension on the support. I did most of the work with the jack removed for more room. When going back together I just jacked the engine back up into position. It is important to choose boards that have minimal knots to make sure that they do not break. I had no problem with standard pine but if you wanted to spend more for either “clear” lumber or even oak, that would be stronger. I used some scraps I had around. To raise and lower the new transmission I used a ratchet strap over the main cross piece and did the change entirely by myself with little problems.

      Reverse lights: As has been posted by others, the pin positions are more important than the wire colors, although the colors are mostly consistent, especially for the gasoline engines. I may have missed something where the terminals were called out for the backup lights, but thought that this photo may be beneficial showing where the Black/Green and Yellow/Blue wires were located in the connector. Just connect them to the backup light switch (after doing the other wiring under the dash) and there you are.



      I also cut the Yellow/Blue wire going to the ECU to avoid problems since this circuit was being used for something else now. Another hint I read somewhere; the backup light switch has the same connector as the brake pad wear sensors. You can cut one off of an old brake pad like I did. Works great.

      Shift Boot: The one supplied with my kit was in pretty bad shape like some of the other photo’s I have seen on other conversions. I am not sure how long my solution will work out but seems to be fine for now. I cleaned the boot with isopropyl alcohol and then sprayed it with 2 coats of FlexSeal. Not like new, but much better than it was.

      I hope these comments useful to others. There are many fine threads out there but seem to miss a few options that can be taken if you are not changing the ECU. Some of the points I made were addressing things that took me a little while to figure out that were not detailed in the threads I read and I wanted to give back a bit.

    2. 06-28-2012 03:07 AM #2
      Hey I'm new to the community here, but I've been on the site many times and its helped me out. I'm having trouble finding information on this tranny swap, because i have a mkIV vr thats an auto, i have the whole car for a swap but the recipient car is a manual 2.0l, i know i would need to swap the cluster and ecu, or find a manual ecu. aswell as clutch master cylinder, but would the shift cables be the same? and if its already got the relay for the reverse light and cruise do i need to splice a wire from the ecu into one of those wires? any help would be appreciated, thanks

    3. Member CoolAirVw's Avatar
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      85 Jetta TD sold 2001 Jetta Tdi, 2000 Jetta Tdi
      06-28-2012 12:56 PM #3
      So you reused your ECM with no changes? I assume your left with lots of codes?
      Auto trans fluid change or flush will not make a trans fail. Stop spreading the wives tale/urban myth.
      ASE Master Certified Technician with L1 Advanced Diagnostic Rating Recently passed ASE certification for Light Diesel repair.
      www.KansasCityTdi.com

    4. Member CoolAirVw's Avatar
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      85 Jetta TD sold 2001 Jetta Tdi, 2000 Jetta Tdi
      06-28-2012 12:57 PM #4
      So you reused your ECM with no changes? I assume your left with codes? More than likely if you were to get a manual ecm your "flare" might go away.

      My tuner said he might be able to reflash a auto ECM with manual software, but it would be experimental.
      Auto trans fluid change or flush will not make a trans fail. Stop spreading the wives tale/urban myth.
      ASE Master Certified Technician with L1 Advanced Diagnostic Rating Recently passed ASE certification for Light Diesel repair.
      www.KansasCityTdi.com

    5. Junior Member
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      2001 Jetta VR6, Wolfsburg 1.8T, 2004 Durango, 1990 Miata 3.0V6, 1966 AH Sprite
      07-23-2012 10:40 PM #5
      OK, so after making sure that everything was working correctly i decided to go ahead and swap the ECU in an attempt to get the flair to go away on shifts. Success!!!. Other than the re-coding of the immobilizer, etc., as described elsewhere and adding the connection between the clutch switch and the ECU everything was set to go from the other posts. The Auto ECU does set errors due to there being none of the sensors or controls that it is looking for. That kept the CEL on, but everything worked fine otherwise.
      In addition to the flair being gone it is also easier to drive away from a stop. There seems to be some "lost motion" in the throttle linkage implementation for the automatic calibration that is not there on the manual ECU, coupled with a slightly different response curve that makes things work out much better. Only having it installed for a week it is hard to say but the fuel economy seems to have suffered slightly, but that could be me playing with it more. Bottom line is that i recommend it.

      Basic Steps as follows:
      1. Remove Auto ECU
      2. Install Manual ECU
      3. Connect One side of the clutch switch to the same common as the brake switch pin 2 (blu/blk).
      4. Connect the other side of the clutch switch (CVVV) to pin 39 (red/white wire) of the ECU. I used a now unused red grey wire that used to go to pin 11 on the TCU, but you also can use the connector right above the relay panel as described in nosborn94's writeup (link to p. 4 below) in a comment from sp1249 on page 5
      5. Update the immobilizer (you will need the VCDS software or a friend at the dealer for 5-8).
      6. Adapt the Throttle body
      7. Set up cruise control.
      8. you can try to configure an Auto ECU to Manual but I gather that this will only work for the Diesel controllers.
      Your done. Took me a couple of hours to finish up.

      Please take the time to check your individual wiring against the Bentley before you start. I found most of the wire colors to be correct in other posts of similar (gasoline) cars for the most part, and the pin numbers were correct, but it would be nice to not have any surprises with the smoke leaking out so check first. A good review also helps you to understand what you are doing, at least it did for me.

      I did make an error on the fluid I used. Just changed it yesterday to the Penzoil Syncromesh ($7.99 / qt qt Advanced) and seems to work well but still have a little crunch in second from time to time if I am a little late on the clutch especially at high RPM. Maybe it needs some time to work into the syncro's. Time will tell.

      For a great discussion with lots of details and pics see http://forums.vwvortex.com/showthrea...)-silver/page4. He has done a great job of documenting his entire process for a 2.0, but most of it applies directly to the VR6. The purpose of my post is to break it down to a more simple summary in case you are overwhelmed by all the detail on most of the posts. It really is not that difficult, but as coolairVW said in one post, the brain work is one of the hard parts. But realistically, I don't know how you would put together a decent set of instructions without all the detail. Read up before starting, and many, many thanks to those before me.

    6. n00b
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      2001 Jetta VR6
      09-21-2012 03:22 AM #6
      Hello, I am hoping you're willing to give me some more details in regards to switching ECU's from the auto to manual on my 01 MK4 Jetta VR6. My good friend and I have come a long way with this project and do not want it to go to waste. I want to finish the tranny swap the right way by switching the ECU's over to prevent the idle flair when shifting, and the small lag when taking off from a stop. (I've read about them)
      I have confusion on how to connect the clutch switch to the brake switch, and how to update the immobilizer. Also don't know what you're referring to when you say "adapt the throttle body".
      I would greatly appreciate your help bro It would mean the world to me if I get this thing finished after all of the work we've done.

      PS: Are you willing to talk to me about this over the phone? It is my birthday tomorrow (the 21st) and we are trying to finish this project before the day is over. (Getting the car ready for a VW car show on Sunday)

      Thanks for any help,
      Curtis

    7. Member Serpent7's Avatar
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      07-25-2013 12:38 PM #7
      I have a 2001 Jetta vr6 auto that has intermittent transmission shifts. I am considering swapping to a 5 speed. Reading this post has inspired me! Before I start I was thinking about putting a parts list together and sourcing them before I get started. Can anyone help with that here? At least a list of parts to get the 5 speed mobile. Thanks
      The best wife in the world...

      Looking for a single, or double cab, any year, any condition... Contact me!

    8. Member CoolAirVw's Avatar
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      07-30-2013 03:22 AM #8
      Seems like you could get the answer to this simply by reading this thread, but here's a short list..

      trans and everything bolted to it including shifter parts and mount bracket, reverse light switch and reverse light switch pigtail harness.

      axles and axle bolts.

      clutch pedal assembly, clutch pedal switches and related Pigtail harness's.

      Brake pedal (don't have to change this, but it makes the conversion nicer)

      Engine "tin" that separates engine from trans

      Clutch.

      I have never converted a VR6 but you'll probably need a computer to make it right. Changing computer require some "stuff" to accommodate the immobilizer.


      Also read this monster thread..

      http://forums.tdiclub.com/showthread.php?t=151516

      The info in this thread is specific to a tdi engine and although most of it will be "dead on", some of it wont apply.
      Last edited by CoolAirVw; 07-30-2013 at 03:25 AM.
      Auto trans fluid change or flush will not make a trans fail. Stop spreading the wives tale/urban myth.
      ASE Master Certified Technician with L1 Advanced Diagnostic Rating Recently passed ASE certification for Light Diesel repair.
      www.KansasCityTdi.com

    9. Junior Member
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      2001 Jetta VR6, Wolfsburg 1.8T, 2004 Durango, 1990 Miata 3.0V6, 1966 AH Sprite
      11-07-2013 06:28 PM #9
      Just getting back to the forum after a long absence and noticed this question. In my case I found that the axles were the same between the VR6 auto and manual trans.

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