Sounds like a problem with your engine rather than the way it is mounted to me. Vr6's are well known for being a really smooth engine. I've got poly mounts in my car and it hardly vibrates.
I am trying to achieve this in my VR6 Corrado, but nothing seems to work. OE motor mounts still seem to transfer vibration from the engine to the cabin, especially at start up, and anything more rigid is likely to make it worse. Is it possible to isolate the engine from the cabin in these cars or is that just the way they are?
You can dampen vibrations by installing more sound insulation on the firewall and footwells.
As to eliminating it all together, I doubt it, as at the end of the day they are 20yr old cars with 20yr old technology. They just had not achieved the levels of sound and NVH newer cars have.
If the floor jack didn't reduce the vibration, most likely it's not the mounts. As far as the clutch, if put it in backward, it would make noise and will not work properly( at all) If you got transmission bolted to the engine, then clutch is align to the input shaft.
Here are few things to check, back to basic. Last tune up, spark plug wires condition, check compression, cap and rotor, if its a dist vr6. Last time fuel filter replaced. Good grounds and power wires, check charging system. Sometime sensors, especially ECT sensor could be funky, or dead 02 sensor, last time you clean the t-body and idle control valve. Make sure the egr working properly and egr pipe is not clogged. Lastly aged injectors can cause rough idle. You can clean them or rebuild them if you can't buy new injectors. How does the engine idle and perform. Lastly check if there any faults store in ECM.
The problem occurred after the chains/clutch/HG was done. It idles like it has big cams but they are stock, where it used to idle smooth as butter. It seems to be loping, and the timing of the sound of the exhaust isn't consistent, like its slightly stumbling, but not too noticeable. Is there a relatively easy way to check the cam and distributor timing to be sure its dead on without a complete disassembly? If the cam timing is off what would the typical symptoms be?