Try shimming the starter. Shaving the critical areas is not likely to stop the rubbing. Typically, the starter pinion nose castings are not an exact science, to put it kindly. Plus, the blocks can have some variance in them too, depending on the line bore of the crank journals and it's relation to the bottom of the block. This is why rebuilt starters always come with the shims, because half the times they need them. GM didn't really build these cars and engines with a lot of precision, and relied on make do engineering to make the parts fit together good enough to work. You need to do the same when you rebuild one.
Of course, I am assuming that it is rubbing where the pinion nose is by the ring gear teeth. If it is on the back of the flywheel that it rubs, then you probably best served to clearance the starter pinion nose so that it does not hit the flywheel.