After reading your post again, you asked about code/spec. Do your contract documents give you a code to fabricated by? If so, that should be the governing code(usually D1.1). Then I would say that you have referenced the right paragraph for your repair of mis-located holes.
Is there anyone who can set anchorbolts correctly anymore? We have laser levels and all sorts of fancy tools that the old guys years ago didn't have but now we can't seem to get anchorbolts set right anymore.
We have a job in the shop now that has the anchor pattern set 90 degrees off from the anchorbolt setting plan and now we have to fix these W14 x 550 bracing columns by cutting off the 4 3/4" thick baseplates and rotating them 90 degrees to match the mis-located anchorbolts.(oops, "anchor rods") For some reason it's not as much fun to weld these the second time.
John Wright