Take this with a huge grain of salt as I'm stepping way outside my comfort zone... but if idle is crappy when hot, only, to me that suggests the idle mixture isn't quite right. If I'm not mistaken, idle mix on EFI systems is typically controlled by an Idle Air Control valve/system which is basically a solenoid operating a valve to let less or more air into the mix (thinking of what I know of the GM EFI systems and based on crap idle problems with my 03 WRX) -- as well as by the O2 sensor, and either a MAF or MAP sensor. If it uses a MAP sensor like GM, then vac leaks would wreak havoc (probably more noticible at idle). As the other person stated, the throttle position sensor (TPS) lets the computer know to go into idle mode (again generalizing from what little I know of GM TBI) so if that is horked, you may not even be in idle mode.
I don't know much about the Chrysler inline 6 EFI systems... but with the GM there are a list of diagnostics you can perform to find problems with each of the sensors that the computer doesn't -- or can't -- detect. The GM system is pretty sophisticated in its error detection and reporting, but again, no clue about the Jeep stuff. What I am talking about is taking a Multimeter and measuring resistances or voltages on sensors.
Don't know if any of this helps but I guess the bottom line is, I'd be leery of trial and error troubleshooting as it can get expensive. The more you can methodically measure and test with anything electronic, the quicker and cheaper you can find and fix the problem.
Michael