My 1-2 shift to me is too early. It's shifting at 40 mph can't remember the rpms but when it shifts it drops low enough to lose acceleration speed. I've tried adjusting the wot shift point with my tuner (sct x4) but it has made no difference. I did notice though that it is only seeing full throttle as 97%. I've tried doing a full Kam reset and relearn, also tried the key on, press pedal to the floor and wait till the check engine light flashes.

Any ideas short of replacing the accelerator pedal position sensor?

 

1-2 at 40 isn't really low, that's over 4000 rpm.

Do not set the WOT shift any higher than 5000 rpm.