UNFORTUNATELY, there are several manufacturers out there making those (same specification) master cylinders. UNFORTUNATELY, some of them use varying length castings and even castings having port bosses cast into both sides, with only one side drilled and tapped for the tubes.
I have seen some of the castings that are extra long and extra wide at the front. While they fit with no problems on the 94-04 Mustangs, those who retrofit them to the early cars can have issues.
I would hate to tell anyone to grind the end of the master cylinder to fit, as there is no telling where the bore actually ends. Twelve thousand stops at 1,100 PSI may be fine, but the last (non-completed) stop when the car needed 1,103 PSI to stop may blow out the ground down bore.
So, your options are:
Angle the booster UP.
Angle the booster to the PASSENGER SIDE.
Dent the shock tower.
Install a Mustang II front end.
Try another master cylinder for same fitment, but shorter, like Ron's.
Probably ten other ways to get there, for those who are creative.
And, remember, those spacers between the booster and firewall can get bent or the firewall can get bent when tightening the booster nuts. If you tighten the nuts on the driver side tighter than the passenger side, it can cause the MC to angle towards the wider part of the shock tower, causing fitment issues. Same happens if the bottom is tightened tighter than the top. Lots of installer induced issues can crop up.