I rebuilt my transmission at one of the tranny clinics, when I got it in the car, it shifted great but whines same as yours.
This is what I've been told, because I had to replace the main bearing, the pinion depth has to be reset, the stacked gaskets. Not sure if I need more thickness or less to set it at the right depth and stop the whine.
Haven't researched how to fix it yet, just put in a different transmission for now, but would like to get the other one fixed....it shifts so much better, but I couldn't handle the noise. I've also been told that it won't damage the transmission to run it this way, but too annoying for me. You said you took yours apart, maybe the pinion depth is off on yours too.
Hope this helps, someone with more experience may have more info, or correct mine
Jeff