You are playing with the stock rear and complaining it is having issues?
There is a reason there are so many freaking bolt-in choices for these cars (12-bolt, 8.8", 9", Dana 60, etc.).
As for the trans, did you cheap out on the rebuild? Who did the build? There are several good places than can build a stout 4L60E...or of course you could toss in a 4L80E as well, but that's one heavy beast of a tranny. TH350/400 would work too, or a Glide.