we recently replaced our transmission with a used one from junk yard. the tranny we bought whines when it gets hot? any clue what this could be?

 

I just rebuilt my transmission. I got a whining sound on two different occasions from a bent flywheel, and the flywheel cover hitting the bolts attaching the flywheel to the torque converter. The frequency of my whine was associated to the engine speed.

Get under the car while the car is running and try to determine if it is coming from where the torque converter connects to the flywheel or if it is from inside the transmission.

It could also be a result of low transmission oil.

Other possible issue might be:
Did you use a new torque converter? Old transmission and/or tc might have had bad oil or water in them.
Did you connect up the transmission oil lines correctly to the cooler? Oil cooling efficiently.

dlm4ut