#09-005-05 TSB done, now ?'s

[rotwiler]

I have a 06 300 with a 3.5L. For the past few months I would get a rough engine feel at times and sometimes on the highway etc the engine would throw a SES light and lose power. Then all would be ok after a few seconds and would be fine for a few more days. Took it to a dealer and they performed a TSB #09-005-05, where they rotated the valves and ran some combustion cleaning stuff through the car.
When I left the dealer the car ran great, my mpg went up from average on highway of 23-24 to 28 on the EVIC and felt like the car had more power than before. Then a couple days later, I started to notice the car shifting different than before, sometimes seems like it waits to shift or doesn't down shift like it used to..on flat road at around 40 mph area if I punch the gas to the floor, sometimes it just barely takes off and doesn't kick down like it used to. It's been hot here(in 90's) and I have been using A/C now, but I tried to not use it the other day to see if it was just the A/C running full that is taking away some power..but I don't think it is that...even at a idle I feel a random stumble every once in awhile with the engine.. Just seems odd the first day the car felt better than ever and a few days later it starts to act up. I haven't threw any SES lights since the repair.
Anyone else with simular issues or had them fixed, I'd appreciate it. My 36k warranty is almost expired and want to get this fixed before it is up. I know they should repair it after the 36k warranty since I complained before it was up, but want to get some ideas before I go into the dealer. Thanks for any help.

[Northern300c]

they reset the computer so everything will be fresh. This is when it seems to be its peppiest but through adaptive learning, it tailors the throttle to your overall driveing habits. Search for throttle pedal recalibration.

Also, with the AC on, you will feel a stumble when the AC cycles on and off. It will drop the engine rpms a bit as it starts and the engine computer will compensate for it.

sounds relatively normal.