[JLemieux]

I must take issue with all of the "Forced flashing" of the PCM that seems to be going on in this post.
For the super charger install, this is exactly what needs to be done. For all of the others doing this to their non-supercharged Jeeps, you are only making your engines run worse until the PCM has adapted the the fuel right back to where it was before you "Force flashed".
I think the piece of information that has been missed here is that adaptive learning is an ongoing process. It changes to current conditions of your engine.
If you have a cracked vacuum hose and a small vacuum leak, the O2 sensors see a short term lean condition and trims the fuel a little bit richer. This is referred to as "Short term fuel trim" or STFT. Since this cracked vacuum hose is not going to fix itself, this lean condition continues to exist and the PCM sees the O2 sensors still lean so it changes the "adaptive memory" to a richer mixture to compensate for the long term lean condition. This is call "Long term fuel trim" or LTFT.
The adaptation is different for every throttle position and load combination and is constatly being updated for current engine wear, sensor condition and any other item that will change the air/fuel ratio from where the PCM whats to see it.
So let's say you typed a 10,000 word essay on you word processor and didn't save it. On word 9,999 someone resets your computer (Forced flash). You get to type it all over again, but in the end you still have the same thing.