That's what i thought you were saying.
that doesn't leave a lot for it to be. You have your wheels and tires balanced properly. It does the vibration no matter what gear your in starting at a certain speed, not engine rpm, that kind of takes out the worry of the pilot bearing. So transmission forward is ok and your wheels are ok. Not much left between those two points.
You have a tailshaft housing with its bushing and seal, the driveshaft with u-joints, and if you screwed with it, the pinion flange/pinion nut/crush sleeve and pinion gear. Did you take the pinion flange off for some reason?
As far as that goes, did you leave the rear end on the car during this?
When you dropped the transmission, did you install a new tailshaft housing seal and bushing? Like
@90sickfox mentioned, this could produce a nice amount of vibration that would travel right through the new crossmember.
You said you had the driveshaft balanced and runout checked, right?
We really are getting past my limits knowledge here with this one. I suppose it's possible that some other thing just had bad timing to go out on you too, but i doubt it.
It just sounds like this would be in the driveshaft area of the driveline, from the ts housing to the pinion gear.
I'm going to invite a couple more people to your thread to see what they might know.
@madmike1157 @Boosted92LX @hoopty5.0 @RangerJoe