I've swap main bolts for studs after having new main caps installed on my first 400 stroker motor, not the same motor but both yours and mine have two main bolts and both had ARP fasteners like yours. I did measure the main bore before and after and saw right at .0002 differences, not enough for me to worry about when I had over .0035 clearances to start with I think the last perfect man on earth is not here anymore, he is sitting beside his father in heaven, according to the bible I believe. My message is you should have discuss this with your engine builder when you discovered the error, he may or may not have fixed it or told you why, if he diecided to ignore youur desires and put the bolts in instead of doing what you wanted. I'm a firm believer in when a shop makes one mistake give them a chance to fix it, when they make two or more it is time to find a better shop BTW, good shops are a lot harder to find than the not so good ones out there Good luck