I'm playing myself with this platform as well, i'm fairly comfortable tuning GM LSx/LQx stuff, and more recently the Coyote platform from Ford, but i'm a newb with Chrysler stuff.
I have a 13 JKU with the 3.6, and I haven't looked into the 3.8's to see what's different, so hopefully most of the logic remains the same.
Here are most of my attempts, I don't have any engine mods, so I've only changed a couple of stuff here and there, trying to improve gas mileage and power overall, it feels better than stock for sure, I haven't messed with the throttle yet as I don't know how to do that yet, hope it helps to get you started.
http://www.hptuners.com/forum/showth...ning-questions
http://www.hptuners.com/forum/showth...E-using-LTFT-s
http://www.hptuners.com/forum/showth...-s-shoud-i-use