Everything is in! New main shaft, input shaft, and pocket roller bearings. Everything is assembled properly and tripled checked. Shimmed the shafts to Tremec spec.
Lo and behold, it still whines... I filled it with synchromesh. It shifts much better than before, but still whines. Just as loud as before. I'm very confused and kind of frustrated. I spent around $350 for all new parts and fluid, just to end up with the same problem as before.
I don't know if my shifter is contributing to the loudness of the whine, but it certainly sounds like I have a blower on the car. Shifter has no gasket and is all aluminium. I also don't have the boot that goes form the transmission tunnel to the shifter.