Only goes in reverse.

Bought a non-running automatic 1997 F-150, replaced the 4.6L engine with one from a wrecked truck. The engine starts now, but the shifter is messed up. The only gear the truck will move in is a Reverse. What could cause this, linkage off, tranny end of shift cable broke, sensor did not get reconnected, etc. ? My truck is 2 wheel drive and the replacement engine was off a 4 wheel drive.

Engine has nothing to do with how the trans is working.

There could be multiple things. It could be any of the things you listed, but the only way you'll find out is to dig and look. I'll bet it is a linkage issue though.