Adding studs for main caps

IIRC studs are fine thread at the nut end and main cap bolts are not so the torque on a fine pitch is going to change the clamping force and possibly distort the shape. Id torque the new ones down and see if your crank has any drag on it. I know its 'SOP' to align hone (as well as resize your rods for ARP type bolts) but probably not essential.