I saw before and after photos of the Shelby relocation. The differences was about 1/2". As far as I know, the ride height should be the same for either spindle. To the best of my knowledge, I don't ever recall anyone having that kind of problem with the ride height after the swap.
About the only thing that I can think of that made the change might be that the last time the front end was rebuilt, when the bolt for the lower control arm was tightened, the suspension was fully extended. This could add some artificial spring rates from the bushings being locked into place at this location. Now, when you took things apart, you tightened the lower arm at it's normal ride height, taking away the added artificial spring rate. I've seen this happen on a friends 65 Fairlane and also have read about it too. BTW, was the 351 already in place or did you add it at the time of relocating the arms/ The 351W is about 75 pounds heavier.
Rehab is for quiters!