JSS or RPM extreme may be your best help, but I can tell you that your Jeep and the Hemi engine will be two separate computers. I had my LT tuned, and paid a dude 100 for the fee to purchase my vin to put on his HP tuner software, now he can change all sorts of preferences. However, I wanted my Jeeps computer to turn on the cooling fans sooner, but I would have had to pay another 100 to purchase my Jeepís vin.
I am using the Chevy engine computer and Jeep computer, interfacing using a Motech module.
I have been told HP tuners is the most compatible with Jeeps/chrysler/Dodge.
Also see what dacapatain20 did, he has a lot of info in his thread.
Good luck on the swap!