One thing to realize about a stock CJ tailgate if you've got a hardtop on your TJ - the factory CJ latches operate from the inside, so if you close the liftgate and then close the tailgate as would be the procedure on a stock TJ, you can't reach inside to operate the CJ tailgate latches. If you close the CJ tailgate before the liftgate, latch it and then close the liftgate, there's nothing to keep the liftgate closed.
There are a number of solutions for installing nice-looking outside latches on a CJ tailgate, I can post some photos if people are interested.