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.