Issues with 7AT after ECU reset

[DarkJak]

I installed CAI's yesterday and after resetting the ECU I've noticed some peculiar behavior with the transmission shifting.

In higher gears, the revs won't be fully locked in. For example, if I'm in 5th, and the revs should be at 2k to match the speed I'm at, the revs would drop down to ~1k when I shift into 5th, vs 2k, as if it didn't grab the gear. Then, when I give it gas, it would rise up to ~3.5k and pull, but eventually drop back down to 2k and lock in. I never had this issue before I reset, and it's bugging me greatly. I'm afraid the gears are slipping or something like that.

Also, the downshift rev matching doesn't always activate when I shift down from higher gears, such as 5-4, 6-5, and sometimes 4-3. It would just get dragged back up instead of popping up. I loved the rev matching feature and I'm very sad that it isn't always working now. A similar thing happens on upshifts. It won't pop into gear, just kind of drag into gear.

Is it possible that I've messed up the transmission somehow? Or have I damaged some wiring when I took the old intakes out?
I'm hoping this is just an issue with the ECU relearning, but I've driven it for over 2 hours so far and every time it seems to lock or shift more aggressively, it'd only go on to limply shift a few seconds later.

Any insight would be nice, whether it's because there is a TSB for it, or I should just keep driving to let the computer readjust more. I'm afraid that it's a mechanical issue, but I'd rather know that instead of driving around with a damaged transmission and damage it further.

Thanks for any input.