I have to agree - set the throws as close as possible mechanically and then fine tune with End Point Adjustments.
I didn't do this on a recent install for the throttle.
Massive EPA adjustments to get the correct throws.
The throttle stick only worked for half of its throw.
Re did the mechanicals and now the stick works for full throw.
Slight EPA for the max throttle was all I needed.
Good Luck,
KW_Counter