Yikes! Looks like the tenon is really having trouble getting in there. If I were you, I might measure where the mortise meets the bottom of the pickup cavity and then check the tenon to be sure that it isn't reaching the bottom of the mortise. You should be able to figure out (with some trial and error) where the problem spots are. Also, spend some time checking that the neck and body angles are consistent. From your photo, it looks like the problem is actually with the mortise edge itself on the RH side. Very careful sanding is probably the safest...although, personally, I'd use a very sharp chisel to fit things if the bottom of the mortise is level and at the correct angle.