2009 Sierra 2500, Bad Shift Flare after 6l90 rebuild.

Truck is all stock. Transmission failed at 270k miles. Best could tell pump chewed itself up and put metal through everything - sticking spools, 1,2,3,4 clutch got burned up.
Transmission was rebuilt. New GM TECM, GM Reman TC, installed Sonnax zip kit, replaced all friction plates, repaired burnt up 1,2,3,4 clutch.

TECM was reprogrammed by reputable independent mobile mechanic. Programmed new TECM no problem.

After rebuild I have a flare during the 6-5 downshift. I logged the data best I could, pretty new to HP Tuners. It shows the flare happening after the shift completes from what I can tell.
The 6-5 downshift flare happens very consistently, I can purposely make it do it, after about 4 or 5 shifts flare occur, you can notice that flare is a little different each time (adapting), then after the 4th or 5th shift the downshift flare is gone. I can drive can keep driving no matter how long after this and it will no longer do this flare.
Once I key off and restart truck after controllers powered down, the flare thing starts right over.

Also get a intermittent flare at 3-4 upshift, this one I can't get to do as consistently so haven't got it logged yet. The 3-4 upshift is worse though, it will yoyo back and forth multiple times before going back to normal operation, same thing though, after couple times doing that shift it will no longer happen the rest of the time driving until truck is restarted.

So attached is 6-5 downshift logged for 5 shifts after truck was restarted, the first 4 shifts show to flare in them, then 5th time doing the downshift the flare is gone and will no longer happen.

The flare does show up as transmission slip.

Any suggestions?
Is there any way to log more specific parameters to pinpoint what is happening? (like solenoid current, circuit pressures?)
Possible mechanical issue or electrical/electronic?

Any help is much appreciated!