I don't know if Jamies Jackpots are like his tuned Rush slipon's but if they are the left side is choked down considerably and acts more like a 2 into 1 where the left side has lots of backpressure compared to the right.....If that's the case, then there should be no reversion problems with stock head pipes when using his Jackpots with autotune.
Jamie makes a great "power package" where he offers tuned exhaust, fueler(PCIII or PCV or Thundermax) A/C and exhaust all together in one simple and not too expensive package. If you order it as a package the fueler will be preprogramed with a base map that is really close. If you include autotune in the package at the start, then you won't have any issues at all.
If instead you order just the fueler, then you need to discuss it with him and describe your exhaust and A/C so he can select the best base map.
The fact remains, if you are running really low restriction exhaust with stock head pipes, you will most likely experience an error when reading the rear 02 sensor in autotune/closed loop. For you guys with cats incorporated in the head pipes, there won't be that particular problem no matter how unrestricted your slipons.
To make things really insteresting, in the future expect to see another 02 sensor soon in the pipe located AFTER the cats.....That sensor will prevent you drilling out the cats...Well, it will prevent it until guys like Jame come up with a fix