Eh the diffs another story :)
I get the main whine even when stationary.
The throwout arm is just kissing the floor (shoulda given it a tap with the ball-pien when I had it out :( ) but is this enough to make a high pitched whine? I thought that'd cause a more rattly buzz type noise. Hmm ill check again.

If the throwoout arm isnt all the way back would this cause it? maybe the floor is stopping it from going all the way back

There is still a different whine when gearing down that ive experienced in my other a series box and thought it was just par for the course of an old gearbox, still works fine...changes are smooth ect...just noisy!!