Vibration problems after T5 swap - almost resolved

Quick re-cap, I had vibration problems over 2000 rpms after doing the T5 swap. This would happen in neutral with the clutch released and the car at a standstill.

So here's an update:

Took it to a shop, they jacked up the back of the tranny a bit to see if it's anything to do with the crossmember. It didn't appear to be a problem. Then they took off the T5 and just left the bellhousing on with the clutch assembly. There were still vibrations. Then they took off the pressure plate and the vibrations seemed to dissappear. So I got a new pressure plate (free) and they put it all back together. There was still a vibration problem.

So I take the flywheel and pressure plate to a machine shop, he checks the flywheel and says it's fine but he says the pressure plate wouldn't fit on his machine or something. So they put it all back together again and say they give up and can't figure out the problem.

I drive the car from the shop and the vibrations don't seem as serious as they were before. I decided to change the balancer even though the one that was on only had about 10,000 miles on it. After replacing the balancer the vibrations seem even less. Now I don't get vibrations till about 3000 rpms and they are very slight. But they are still there. Maybe this isn't going to run as smooth as the AOD-E did?

Also I took it on the highway and at 4000 rpms there is quite a bit of vibration.

So does anyone have any clue what this could be? I'm stumped.

I took the car to a guy here at R&R racing engines, he works on mustangs a lot and he said it's probably something with the flywheel or pressure plate. He said I could bring him both and he has a new machine that can balance them perfectly. The thing is that I'm so tired of taking this thing apart and I don't have time right now. The shop will want $100 to take down the trans and give me the flywheel and pressure plate and then put it back together. I could spend another $200 on that and it still might not be the problem. The machine shop says that if it's not the flywheel or pressure plate or balancer, and it's still there without the T5 on, then there is a balance problem within the engine.

I'm thinking now is it possible that this is some kind of electrical problem? I have about 15,000 miles on the current spark plugs and 5,000 miles on the wires. The coil appears to be original. Alternator is a year old, doesn't have charging problems. The exhaust doesn't smell rich or anything.

Nope can't be the driveshaft. It does it at a standstill. The driveshaft doesn't spin then.

The motor mounts don't look that bad but I thought they might be a problem. I'm going to get a new trans mount cuz the current one is pretty beat up. We had to grind down the holes in the crossmember so that it would line up with the trans mount on the tranny. But the those two little transmount bolts are still sort of at an angle because the crossmember still seems about 5mm too far.

The only way I could see a disk causing the problem is if it wasn't aligned properly. We used a clutch alignment tool to align it. Does the clutch disk have enough weight to it to even cause a vibration problem do to a balance issue?

Well it still vibrated a bit with the flywheel on but the car was on a lift, but with the pressure plate on the vibration was much more noticeable.

The distributor is still the original one so maybe I should replace that. I want to do the easy stuff first.