So this raised spot that every main has by the oil hole, is this from machining/drilling the oil holes/galleries on the mains, almost like a burr? If so you might not need an align hone, hitting each with a radius'd small hone and working them out by hand might suffice. Id think bad main alignment would've even should up with the looser clearances? You take away .001 to .0015" and now it's to tight? I'd get rid of the burrs (if that's what they are), polish the snot out of the crank and get your .004" bearing clearance back.