Just wondering if you ever found out the problem? I'm running into the exact same issue and have basically checked the exact same things you have. Frustrating to say the least!

 

I had an oscillating vibration that set in after the diff warmed up turns out the person who owned it before me didn't change the fluid enough and or beat the crap out of it as I lost turning torque on the pinion bearing and it let go cursing down the highway lock the rear for a second car rotated and I went sliding through the woods. is there any metal in the fluid? I built a diff that was in good shape ct engineering main cap mod and j's racing pinion collar no vibration anymore hope that's not your problem

 

Still vibrates alittle but a third tire balance and some brek in in my current combination has made the problem livable.

 

bump for update?

 

Just living with it on the street cause its not too bad. There is no noticable vibration at the track. I wish i was motivated to take the car to another level either in style or racing but for now things are stagnent. I treated myself to a steering wheel and soon i will need a new top. Goin back to Sebring in january. If it breaks ill post. Sorry i couldnt posts anything useful.