Crank no start

Chances are the crankshaft position sensor got damaged if it wasn't removed before the transmission was removed. Pull that out and check it first.

I'm skeptical, but there's no arguing with success. Chrysler has very little trouble with their Engine Computers, and it seems strange one would work fine driving the truck into the shop, then suddenly not work after the service was completed. I'd be tempted to reinstall the old computer to see what happens.

Be aware too that when power is lost to the computer, either through disconnecting it or the battery, it loses its memory. Most information, like fuel trim data, will be rebuilt as you start driving again, but "minimum throttle" has to be relearned before the computer will know when it has to be in control of idle speed. Until that is done, the engine may not start unless the accelerator pedal is held down 1/4", you won't get the nice idle flare-up to 1500 rpm at start-up, and it will tend to stall at stop signs. If you run into that, to meet the conditions for the relearn to take place, drive at highway speed with the engine warmed up, then coast for at least seven seconds without touching the pedals.