You bring up an interesting point on the calibration procedure. When I was having my 1>2 shift issues I performed the Adaptive Reset (via HPtuners) but don't recall using AlfaOBD to perform the Quick Learn as explained in this vid,
https://youtu.be/wDmrLD3ph0s?si=zJTl1SpqmQvxQT16
I'll keep this procedure in mind as I've shipped my tranny off for a rebuild, which will include a custom-spec converter.