The main purpose of the bell housing alignment is to get 'dead center' the input shaft of the trans. Of course that would also impact flywheel clearance and starter alignment. While shims are typical on a GM product there seldom required on a Ford, relativly speaking. If the starter does not DISENGAGE smoothly after it's turned off that would indicate the starter gear teeth are 'to deep' into the ring gear teeth. But a 'screetch', hmmm, got me there. Standard issue Ford (like from NAPA) starters are reasonably priced, perhaps you could find/borrow one to test with? Heck, buy it, test it and take it back!
