Greg,

The best way is to use an adjustable blade reamer. Done many this way. Very common problem. Surprised you didnt have thrust issues with the cap like that. You CAN drill it, especially if you have a good solid Bridgeport or drill press, but I have done both and I prefer the "dial in" ability of the reamer. Technichally the bolts dont do anything but provide the clamping force, and shouldnt even touch the cap, but you dont want to over bore the holes.The cap register provides the right fit. Good luck, hope it works out ok.