I had some interference issues with my 5D MkII because the mirror was so large that it hit the back of the Schneider-Kreuznach lens. I had to file off a bit of the rear flange to give the mirror enough clearance to swing up and down. It worked great but then I sold the body.
That does not surprise me one bit. The mirror in the FF body is much larger than the mirror in an APS-C body. I don't like making mods like that if I don't have to.