Black Jack: Vibration diagnostics. Not making foxtoberfest

If it still does it afterwards, try raising and lowering the trans in small amounts with a jack while its running, I had a nasty vibration years back that was from an HPM cross member throwing the angle out of wack on my 3550, shimming the mount height eventually fixed it.
 
Your not moving it ton, and a screw jack might work best, disconnect the trans mounts and do it with it in the air, it stresses the input shaft pre load more than anything as the motor mounts will absorb most of the movement and let the engine move a bit. with mine and the old HPM cross member it needed almost 1/2" of shimming between the mount and the tailshaft pad, mine was very rpm specific but happened in or at out of gear, but was worse on the highway at certain speeds,
 
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I only skimmed the info but it started after clutch and or the work they did welding up the torque boxes and D/S loop, I'd expect its possible it changed the angles just enough. like the tko, the t56 doesnt share the same mounting pad height as a t5 so shimming is pretty important. I would look close at the cross member since stifflers can be assembled a few different ways by the bushings and spacers. I remember chasing a vibration like this this almost exactly with I put in the old HPM one, drove home from work after throwing it in, and it started to vibrate on the highway and it even had the vibration in neutral sitting still free reving by the time I got home. This was way back, stifflers wasn't even a company, HPM had the gold solid cross memeber sold specifically for tremecs, but It was a bind caused by the cross member. Can you measure drive line angles? With the old school hpm cross member not only did it throw off the angles but it also was binding on the tunnel itself, the raised section on the passenger side for the exhaust, clearance was paper thin between the floor board and amplifying the vibration, shimming the mount and extending the body side mount holes fixed it with zero vibration affer.
 
Yeah, I hear you. I remember that gold HPM crossmember from back when I had a TKO, which at the time was essentially just a 3550 with a 26-spline input shaft. This was before the TKO 500 and 600 came along.

I guess what I don't understand is why you were experiencing the vibration in neutral, especially if it was still present with the transmission in gear and the clutch fully depressed. Regardless, I'll eventually work through all of that.

I do have the equipment to measure driveline angles, and I've set the engine, driveshaft, and pinion angles with the Stifflers crossmember installed. In fact, it's the only crossmember I've ever used with the T56. What I haven't done is recheck those angles since installing the driveshaft safety loop. The loop added approximately 1/4" of plate above the transmission crossmember, so I removed roughly 1/4" of spacer to compensate. I didn't measure it precisely, though, so it's certainly worth revisiting.

First things first, though. I need to get this pressure plate checked out.

My regular machine shop said they couldn't balance it without the complete assembly. I called another shop, and I'm actually on my way home now to pick up a neutral-balanced flywheel because they can't do it with my 50 oz imbalance flywheel.

I really don't think the flywheel itself is the problem, unless the three locating dowels are somehow misaligning the pressure plate. After I get everything back, assuming I'm no longer racing the clock to make it to Foxtoberfest, I'll reinstall the pressure plate by itself and see if the vibration returns.

If the shop finds the pressure plate out of balance and can correct it in time for Foxtoberfest, I may just put everything back together and hope for the best. I'll make a quick attempt to check and adjust the pinion angle, but I won't have much time to get carried away with it. That can easily turn into a multi-hour ordeal.