So you used the stock bolts but did you use the plate? The bolts didn't bottom out on my setup and wouldn't have been the cause of the rubbing. It isn't the extra length of the bolts that is causing clearance issues. The only real explanation is the extra thickness created by the back plate caused the bolts to protrude enough to rub on the clutch plate. My main reason for using the back plate was to prevent the bolts from digging into the softer aluminum of the flywheel which had been happening on the previous engine.