I had some free time and all the necessary pics, so I put this little DIY together. Hope it's useful to someone.
REMOVING AND CLEANING A MKIV THROTTLE BODY (THROTTLE VALVE CONTROL MODULE)
The following outlines the procedure for removing and cleaning the drive-by-wire (DBW) throttle body (officially known as the throttle valve control module) on a MKIV VW. The procedures were based on a 99.5 Jetta GLS VR6 and may be different on MKIV cars with different engines (1.8T, 2.0), body styles (Golf, GTI, New Beetle) and from different model years. Specifically, the procedures for removing and reinstalling the throttle body (herein referred to as TB) may differ due to slight differences in the design and orientation of the TB, however, the general removal/reinstallation procedures, as well as the cleaning procedures should be very similar. Please do these procedures at your own risk and be ready to make small adjustments while doing them. Also, please be observant while removing parts so that they go back together correctly.
Before proceeding any further, I must make it clear that the DBW TBs used on the MKIV vehicles are high-precision, electro-mechanical devices. If you damage the servos and sensors which control the motion and position of the throttle valve (also known as the butterfly valve) while performing this procedure, there is a very great chance that your engine will not run correctly and the TB will need to be replaced. Since a new TB costs around $500, this is something that you will obviously want to prevent from happening. Therefore, be extremely careful when performing the procedure and heed the warnings and cautions that are given. I am not, nor will be held responsible if you mess up your TB while doing this procedure.
This DIY is broken up into three parts...
Part I deals with the removal of the TB from the intake circuit. Two methods for removing the TB are given. The first method is the "quick and dirty" method and requires that the least number of things be disconnected/removed in order to disconnect the TB. I did not perform this procedure, so I have no idea how long it takes. Nevertheless, I have supplied it for all the minimalist DIYers out there who like to keep things simple. (Note: If you follow this method, you may notice that the pictures posted for this method do not actually show anything disconnected. Please disregard these inconsistencies. Since I did not perform this procedure, I did not have the appropriate pictures and used those taken after everything was already reassembled. Just follow the written directions, using the photos only as a reference, and you should have no problems.) The second method is the "slow and thorough" method and requires that significantly more things be disconnected. The advantages of this method are that it (1) allows various other parts of the intake system, such as the main intake tube and PCV circuit to be examined and cleaned and (2) unclutters the "workspace", making it significantly easier to remove the coolant lines from the TB. This method is the one that I followed when cleaning my TB and I recommend that others use it as well. If you're familiar with this area of the engine bay, it will take approximately 30-60 mins to remove the TB using this method.
Part II deals with the cleaning of the TB. The cleaning procedure should take 30-60 mins or more, depending greatly on how dirty your TB is and how careful and thorough you are when cleaning it.
Part III deals with the adaptation of the TB to the engine control module (ECM) using a VAG-COM or other suitable scan tool. It is not absolutely necessary to perform this procedure, however doing so immediately following the reinstallation of the TB will help insure the smooth operation of the engine when it's first started.
The tools/parts needed to perform the procedures are:
1) 10mm wrench or socket (to disconnect negative battery lead)
2) Appropriate tool for removing hose clamps. If you have the stock spring clamps, a pair of channel lock pliers works great for this purpose since the jaws are roughly perpendicular to each other (helps prevent clamps from slipping in plier jaws) and the jaw width can be adjusted for each particular clamp size. If you have screw-type clamps, you'll need the appropriate screwdriver.
3) 5mm hex/Allen wrench (to remove TB from intake manifold)
4) Phillips screwdriver (only needed in "slow and thorough" method if removing MAF housing from air filter housing)
5) Flat blade screwdriver (to help remove spark plug wire boots from coilpack - not needed for "quick and dirty" method)
6) T30 Torx driver (to remove engine cover pieces - not needed for "quick and dirty" method)
7) Can of intake/TB cleaner
8) Q-tips or something similar (to gently scrub away the TB deposits)
9) Sheet of plain white paper
10) Paper towels or rags
optional ...
11) New TB-to-manifold gasket. The Bentley manual instructs that this gasket should be replaced when the TB is removed, but more than likely it can be reused. Mine was still in excellent shape so I reused it. If you are uncomfortable doing this, purchase a new gasket.
12) VAG-COM or other suitable scan tool (for performing adaptation of TB to ECM).
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PART I - REMOVING THE THROTTLE BODY
1. The TB is located at the back of the engine bay between the air intake hose and the intake manifold and is indicated by the yellow arrow in picture below.

2. The TB is shaded blue in the picture below.

- To follow the "quick and dirty" removal method, follow steps 3 through 11.
- To follow the "slow and thorough" removal method, follow steps 12 through 30.
QUICK AND DIRTY REMOVAL METHOD
3. Remove the battery box cover and disconnect the negative (-) battery lead from the battery using a 10mm wrench or socket. Secure the lead away from the (-) battery post so that it does not accidentally touch it while you're working on the car.
4. Disconnect the harness connector from the TB. The connector is indicated by the yellow arrow in the picture below.
5. Unclip the coolant hose (red arrow in picture below) and the PCV vacuum-assist hose (yellow arrow in picture below) from the top of the air intake tube.
6. Disconnect the upper coolant hose (yellow arrow in picture below) and lower coolant hose (blue arrow in picture below) from the TB. To do this, use the appropriate tool (pliers or screwdriver) to release the tension from the hose clamp, slide the clamp down the hose and out of the way (for spring clamps, make sure the clamp is moved past the end of the nipple inside the hose or the clamp will reapply pressure to the nipple when released), and then pull the hose off of it's nipple.
7. Release the tension from the clamp securing the main air intake tube to the TB (indicated by yellow arrow in picture below) and then slide the intake tube off of the TB.
8. Using a 5mm hex/Allen wrench, remove the 4 long bolts that secure the TB to the intake manifold. There is one bolt at each corner of the TB, two of which are indicated by the yellow arrows in the picture below. Support the weight of the TB as you remove the last bolt. You wouldn't want the TB to fall - it is a delicate, high-precision device. Note that one of the bolts also secures a ground wire to the TB (indicated by red arrow in picture below). In my case, the ground wire was secured by the lower, front bolt, but a different bolt may be used in your car. Remember which bolt the wire was attached with so that it can be reinstalled in the same position.
9. While holding the main intake tube and coolant/vacuum hoses out of the way, pull the TB up and off of the intake manifold.
CAUTION: Be careful not to let ANYTHING fall into the intake manifold while the TB is removed. You don't want any foreign objects being sucked into the engine when it's first started - this may cause severe damage!
10. The yellow arrow in the picture below indicates the gasket that seals the rear of the TB to the intake manifold. Prior to reinstalling the TB (new or existing), either replace the gasket with a new one or decide to reuse the existing one. If you decide to reuse the existing gasket, make sure to clean it by wiping it with a rag or paper towel to remove any debris or contaminants that may be on the mating surface. (The red arrow in the picture below shows a better view of the ground connection that is secured to the TB by one of its mounting bolts.)
11. If you are replacing the TB, install the new unit by following steps 3 through 9 in reverse and then proceed to Part III (TB adaptation). If you are cleaning your existing TB, proceed to Part II.
SLOW AND THOROUGH REMOVAL METHOD
12. Remove the battery box cover and disconnect the negative (-) battery lead from the battery using a 10mm wrench or socket. Secure the lead away from the (-) battery post so that it does not accidentally touch it while you're working on the car.
13. Release the tension from the clamp securing the main air intake tube to the MAF housing (indicated by yellow arrow in picture below) and then slide the intake tube off of the housing. If you're like me and are paranoid that anything you do under the hood can potentially harm the poorly-designed MKIV MAFs, you may also want to remove the MAF and put it in a safe place. It is not necessary to do this in order to remove the TB, but you never know with these MAFs. If you want to remove the MAF housing from the air filter box, disconnect the MAF harness connector (red arrow in picture below), remove the two Phillips screws that secure the MAF housing to the air filter box (one of the screws is indicated by the blue arrow) and GENTLY slide the housing out of the filter box. There is a large gasket sealing the two which snaps into the opening in the filter box, so it may require some force to separate them.

14. Carefully remove the spark plug wires from the ignition coilpack by pulling the rubber wire boots off of the posts on the coilpack, as shown in the picture below. This may be difficult due to the suction created by the seal between the boots and posts. I used a flat blade screw driver to carefully slide the boots off of the posts. (Be careful not to rip the boots if you do this or the engine may misfire when moisture is present.) I recommend that you mark each wire so that it is reinstalled on the correct post later on.

15. Unclip the spark plug wires from the channels in the engine cover, as shown below.

16. Remove the small engine cover piece with the VW logo on it by removing the single T30 Torx screw, indicated by the yellow arrow in the picture below.
17. Remove the long, thin engine cover piece on the passenger's side of the engine by removing the two (2) T30 Torx screws indicated by the yellow arrows in the picture below.

18. Remove the main engine cover piece by removing the four (4) T30 Torx screws indicated by the yellow arrows in the picture below. As you lift up on the cover piece, you will need to thread the spark plug wires through their respective holes in the cover in order to fully remove it.

19. The picture below shows how the top of the engine should look with the three engine cover pieces removed.

20. Disconnect the electrical harness connectors for the TB (yellow arrow in picture below) and PCV valve heater (red arrow in picture below). Next, unclip the TB harness connector lead from the top of the coolant hose which passes over top of the main air intake tube (white arrow in the picture below) and move the lead out of the way. Finally, disconnect the vacuum-assist hose (green arrow in picture below) from the PCV valve S-hose (between valve cover and main intake tube), unclip the hose from the top of the main intake tube (blue arrow in picture below) and move the hose out of the way.
21. Disconnect the PCV S-hose from the PCV valve on the main intake tube by pushing the two serrated tabs together (yellow arrows in picture below) and carefully pulling the hose off. If you want to also clean the inside of the PCV S-hose (there WILL be oil in it), release the tension from the clamp on the other end of the S-hose (red arrow in picture below), slide the clamp up the hose a bit and then pull the hose off of its nipple. (Note the position of the bend in the S-hose relative to the bolt/nut just to the rear of the oil cap. There should be sufficient room between the hose and bolt so that the bolt does not cut into the hose. There is a depression on the underside of the hose at the bend to provide more clearance. Make sure to reinstall the hose in the same position later on so that abrasion does not occur.)
22. The picture below shows the inside of the PCV valve/heater on the main intake tube. If you look closely, you can see the abundance of condensed oil vapors.
23. Disconnect the upper coolant hose (yellow arrow in picture below) from the TB. The nipple on the TB is approximately 1" long, so the clamp has to be moved up the hose at least that much in order to remove the hose from the nipple.

24. Disconnect the lower coolant hose (yellow arrow in picture below) from the TB. Again the nipple on the TB is approximately 1" long, so the clamp has to be moved down the hose at least that much in order to remove the hose from the nipple.
25. Disconnect the vertical coolant hose (yellow arrow in picture below) from the T-junction in front of the TB/main air intake tube. Next, unclip the horizontal portion of the coolant hose T-junction from the top of the main intake tube (red arrow in picture below) and then move the hose out of the way. At this point, there should be no coolant hoses attached to the TB, nor should there be any coolant hoses or electrical leads passing over the top of the main intake tube.

26. Release the tension from the clamp securing the main intake tube to the TB (indicated by yellow arrow in picture below) and then slide the intake tube off of the TB.
27. The picture below shows the large amount of condensed oil vapor in the main intake tube due to the PCV circuit. I wiped this oil off the inside of the tube with a paper towel. (I can only imagine how much oil is in the intake manifold and elsewhere in the engine. Someday I'll clean it all out.)
28. Using a 5mm hex/Allen wrench, remove the 4 long bolts that secure the TB to the intake manifold. There is one bolt at each corner of the TB, as indicated by the yellow arrows in the picture below. Support the weight of the TB as you remove the last bolt. You wouldn't want the TB to fall - it is a delicate, high-precision device. Note that one of the bolts also secures a ground wire to the TB (indicated by red arrow in picture below). In my case, the ground wire was secured by the lower, front bolt, but a different bolt may be used in your car. Remember which bolt the wire was attached with so that it can be reinstalled in the same position.

CAUTION: Be careful not to let ANYTHING fall into the intake manifold while the TB is removed. You don't want any foreign objects being sucked into the engine when it's first started - this may cause severe damage!
29. The yellow arrow in the picture below indicates the gasket that seals the rear of the TB to the intake manifold. Prior to reinstalling the TB (new or existing), either replace the gasket with a new one or decide to reuse the existing one. If you decide to reuse the existing gasket, make sure to clean it by wiping it with a rag or paper towel to remove any debris or contaminants that may be on the mating surface. I determined that the gasket in my car was in good enough shape to be reused, so that's what I did. No biggie. (The red arrow in the picture below shows a better view of the ground connection that is secured to the TB by one of its mounting bolts.)
30. If you are replacing the TB, install the new unit by following steps 12 through 28 in reverse and then proceed to Part III (TB adaptation). If you are cleaning your existing TB, proceed directly to Part II.
Let me know if you have any questions.
As always, do this procedure at your own risk. I am not responsible for any mistakes in the procedure or those that you make while performing it.
Modified by VgRt6 at 6:39 PM 5-13-2004