Before i would do anything I would check the bearing alignment in the block and cap for mislocated tangs before installing the crank and check for radius clearence on all the mains.Then install the #3 cap with the studs turned all the way in and backed out a 1/4 turn.Take a lead hammer and smack the crank for and aft checking the clearence at the main thrust on each side of #3 and check crank end play.Some times the thrust sides of the bearing need to be conformed to the cap and block.If this doesn't solve the issue then ream the cap holes as others have mentioned. We found a similar problem at #3 thrust and it was actually cause by #5 cap that the bearing was riding on the radius and creating the issue,that's why I suggest you check all mains.