Originally Posted by ColdCase
The jeep adapts to the stock emissions settings so there is little or no long term power gains. Anyone telling you different is a vendor trying to sell you something. You can get the PCM re calibrated to take advantage of your modifications bat sending it off to one of the tuning outfits, about $600. Forget about the warranty, however.
It has nothing to do with emissions per se, it's all about fuel trims.
Adding aftermarket parts, whatever they might be, changes the fueling demands of the engine because of the resultant change in volumetric efficiency. So on a fresh PCM reset, the adaptives are not doing anything because there is no prior memory from the O2s providing feedback to the PCM regarding changing what's written in the VE map to reach stoich. Over time, the trims force the actual AFR to be either lean or rich of commanded AFR , be it stoich or otherwise. This is part of the reason why tunes help so much, because the VE map is altered to better suit the needs of the modified setup. Power is still improved without tuning, but diminished some by the large fuel trims swaying the AFR well lean of stoich.
Can't speak for the newer engines as I have not done datalogging on any of them, but the WK1 Hemis from the factory already have trims in the double digits without any modifications. This is likely the factory's way of squeezing mileage out.