Well, it's not the first time I've heard of ATF in a manual. It's been used for years in place of power steering fluid. I just recently quit using it in my '67 PS, because it gets a little confusing when you have a trans leak AND PS leak.
I think I'll just go get some Royal Purple 75W-140 for the diff, and will think of the 75W-90 as a flush.

If it helps with the whine, it's worth the money. I never hear it with the windows down, but it won't be long till I have to start rolling them up.

I think I will probably also go with Royal Purple 5W-20 for the trans. I don't have any shifting problems, but just hate to go over 100k miles without changing it.
Just out of curiosity, what do your manuals list for fluids?