My machinist said that is a common problem when using main cap studs. The main stud needs to be shortened about .250" and use a 12-point nut. Then the oil pump must be touched up with a grinder, checking the fit until enough clearance is obtained. Those modifications should give the needed clearance. I use OE main cap bolts and ARP washers and this particular problem never occurred.
My engine is equipped with a Melling Select 10552 oil pump and I was more concerned about the clearance between the oil pump and the steel collar on the oil pump drive shaft. The steel collar on the pump shaft is larger in diameter than the OE nylon collar and it has about .015" - .020" eyeballed clearance from the main cap. That is goodenuff.