It's Always a Problem: one fastener or the other (now rod bolt):

[Dibbons]

Finally removed the connecting rod caps from the 340 connecting rods after I had a shop install ARP rod bolts and recondition the large end. I noticed right off the bat one nut could not be removed by hand after it had been broken loose with a breaker bar. First tried a different nut but same interference. Brought out the trusty magnifying glass and found on that particular bolt the first two threads are squished. Forutnately, I mistakenly purchaed two sets of small block ARP bolt sets so I can "borrow" one from the complete set and take care of the problem. Unexpected glitch to say the least. Doesn't really show up in the photo, but it's obvious to the naked eye.

 

[R413]

You might take the road and new bolt back to the machine shop and have them do this. Then Recheck the roundness of the big end. ARP bolts are tight fitting and may change the round shape of the rod.