I'm in the same predicament.

I have a 94/95 vr6 with the same intermittent surging/missfire/Holding back. Some days fine some days not. Worse when wet or hot I think.
On a good day It still fly's.
I have new leads,plugs,coilpack. Each time I replaced something it went a bit better.Although it could just be my brain tricking me as the car usually goes better at high revs anyway, And I usually would give it a good thrash after replacing the part.
The plugs were the first thing I replaced. I should have done the coil pack and the leads first. I think my plugs might now be fouled up because they ran with the original faulty leads and coil. I am going to replace the plugs one more time(I'm going round in circles) Also I suppose a MAF is possibly the next thing to try. I've just got vag-com sorted on my mac and have some instructions on there website how to do a MAF test. Which I'm gonna do this weekend.
Also recently clutch, mounts and timing chains.
Clean Throttle body, Clean ISV, Clean air filter( I have a sponge filter in the factory box what do you use?)
We should stay in touch until we get to the bottom of it!!!!!!!