If I were to shave the holes, I would have them welded. I don't have a welder, and I would definitely not use bondo. So I would not be doing it myself. That's several hundred dollars I would rather spend on more suspension stuff, or a header to get rid of this damn manifold rattle, or HID, etc. But like I said, I don't like doing non-reversible mods anyway.
The holes are approx. 1/4" for the bolt holes, 3/8" for the guide pin, and 7/8" for the wire harness. But like I said, all the hole plugs I've tried are either too big or too small, except for the 7/8" plug which fit perfectly.