I'd bought an '07 road king new, put some mufflers on after the first week/1000 miles, and ran it that way for a while. I wasn't exceedingly happy so I got a filter assembly and a PC-III with a canned map for the combo. It ran so poorly it wouldn't hardly pull 90 mph. Overly rich. I did some studying and determined the problem was that my adaptive fuel values were getting in the way. They'd been developed from running with just the mufflers on. There were two ways I could see to get them reset. One would be to visit the dealer and have them use their digital technician. The other would be to re-install all the stock parts and ride comprehensively for a while. I opted for the second method. It worked well-enough. When I put all the aftermarket stuff back on all at once, the canned map worked much better.
So I rode it like that for a summer or so.
I discussed my findings with the nationally-known shop from whom I'd got the air cleaner and PC-III/map, and suggested he reset the AFVs prior to developing the canned maps and to inform his customers to reset their AFVs prior to installing the stuff. He said the adaptive fuel values wouldn't/shouldn't make that much difference but I can tell you first-hand they do.
But I still wasn't enthralled with the setup so ordered a TTS kit. Just the canned starting map from/for the TTS was night and day better, and after v-tuning it a little it was great. I've been a happy TTS user (2 more units/bikes) since then.
If you use any sort of piggyback controller and it disables closed-loop operation in any way, shape, or form, do not ever temporarily go back to closed-loop operation with any other parts that your ECM isn't calibrated for. It will change the "tune" that the piggyback is working against.