With your engine I would use the bolts, since that was what it was align honed with. The Studs, because their shank is fatter then the bolts are sure to push those caps out of their alignment. If you want to use the studs, redo the align hone for them.

Im sure your measurements will confirm that. You really don't need the studs though with your combo. But if the blocks still bare, use them and rehone.