I bought a 1997 4 door tracker with a blown engine. I took an engine out of a 97 2dr 5 speed and put it in the 4dr.  Everything went fine, the engine started and runs great, but the trans won't work.  The torque converter is turning and the trans is full of oil.  I can hear the engine speed up when I put it in drive, so I assume the ECM is working fine, but the wheels don't turn.  I removed the trans cooling lines from the bottom of the rad and no oil is coming out of them.  Does this mean that they cooked the trans and blew up the engine at the same time or have I done something wrong.

Sounds like a fried trans to me. BUT, I do know the 4-speed auto is ECU controlled. Have you double checked the wiring? Perhaps something got un-plugged during the swap? Hopefully someone with more auto trans experience than me can pipe in.

I'm hoping it's something simple like a wire.
Thanks