Where are you getting the motor? If the trans is still in the vehicle your pulling the motor from take the trans too along with the computer and harness.
But yes you can get the trans from a junk yard if you can find one. TJ's are a diamond in the ruff at a junk yard and you will be hard pressed to find one there.
Daveysjeeps.com is a jeep salvage yard in OH with anything you would want.
You also don't have to have the motor trans from a TJ.