Never seen it done before, but I can tell you that a host of things will be different including most likely A/C mounting points, power steering mounting points, alternator, etc.
The short block is the same, but the way the things bolt on it is likely very, very different. The easiest way would be to get the short block from the Challenger (just the engine) and swap it into your JK, bolting on the JK accessories and brackets to the Challenger block. That is of course assuming that the mounting points on the Challenger 3.6 block are the same.
Given that there are so many unknowns here (and I didn't find any into on it on Google), I think you may have to be the trail blazer on this one.