I also had a multitude of things not lining up on truck #2 not too long ago. The holes did not line up and the I had a hell of a time getting the booster lining up so the pedal shaft would line up with the hole in the cab...I found a new language during installation of the "bolt right in" power booster unit. I even had not even installed the fenders and motor at that point.

PATIENCE MY MAN
Steve