The Fordomatic linkage set-up directions are shown in two places in the car manuals - and it isn't all fully explained in either one. Because the pedal height (off the floor) shows up in the transmission manual - and not the shop manual - it is often overlooked. If you don't have something like 4-3/8 between the back of the gas pedal and the floorboard - the linkage probably won't progress far enough into the "kickdown" slot to make the shift.
As the pedal advances toward the floor, the carb primary throttle blade moves to wide open - and then the linkage continues to travel in the "kickdown slot". It is made so that you can get WOT - without continuing into kickdown. If the pedal is too close to the floor (a very common problem if someone has just been fooling with the kickdown rod length alone) then you can get a rough part throttle shift.
When I put a later type carb on my '56 - the primary throttle rod position on the primary lever - the hole to mount it - wasn't at the same point as the "teapot". It therefore didn't have the same rotational travel as it went to WOT. So, after some measuring of both carbs - I drilled an additional hole in the "newer" 4160 model Holley so it would match the travel of the old carb. You could then use the factory set-up sequence.
Steve Metzger Tucson, Arizona