First time rebuild problems-trouble upshifting

My only guess is the problems are due to the load control servo. The front servo needs to apply quickly for a good WOT 1-2 shift and release quickly for a clean 2-3 shift. I rebuilt a 727 for a buddy several yrs. ago and used the load control servo and we experienced a lot of what you described. It's been so long I don't remember if it had all the issues yours has but I for sure remember the part throttle 2-3 shift was real harsh (overlapping) but fine wide open. I dropped the pan and swapped it out for an old style servo with 2 springs and it shifted great at every speed and throttle opening after that.

I can't guarantee the old style servo will fix it but that's where I'd start.

BTW: what ratio front band lever are you running?