Transmission problems...I think

I have a 2003 ford explorer xlt 4x4 it has about 70,000 miles on it..I
noticed a while back that it wasnt shifting right (I could feel it jerk a
bit as it was changing gears) and it made a whining kinda sound as I was
driving. So I take it to aamco and they say that the tranny is ruined and
they need to rebuild it. So $3000 later I have it back and it seems better
but after it is being drove for a bit it shifts kinda funny and still has
the sound. Actually the sound seems a little worse now on occasion. I am
definatley taking it back to aamco but I was just curious if anyone here as
any experience with a problem like this. Is it deifnatley the tranny or
could it be the rear end also possibly? Any input is appreciated.