That's common on most all Ford engines using ARP main studs, even most V8's. It is perfectly acceptable to grind or machine the stud shorter to where no threads stick out past the nut when torqued and grind clearance on the pump body. During the 5.0 Mustang craze, all of them had to be done that way and if you used a high volume pump, you had to dimple the oil pan as well because the pump body was fatter and taller. That's just one of the tricks of the trade when using non-stick, high performance parts sometimes. Those mods wont hurt a thing....!