Yeah, if you aren't getting a signal from the crankshaft sensor , your computer will not allow your Jeep to start... It senses where your flywheel is with respect to your motor.
Are you sure that the sensor was put back correctly? I believe it would be located on the bellhousing... Near the top...?
So when you removed and put the transmission back in when swapping the flywheel, you may not have remembered to get it connected or possibly just not correctly...?
Not trying to be harsh - just tryin' to help!