if it's just a gap, fill it with putty, thick paint, or gap-filling superglue, then sand smooth.
If the parts are uneven (one part is higher than the other) and there is absolutely, positively no way to correct the problem before assembly (i.e. warming and warping the parts, removing alignment pins, adding some styrene or putty) your choices are pretty limited. The best way is to bite the bullet, sand the joint smooth, and rescribe the panel lines with a X-Acto knife. You can use tiny drops of glue to replace the lost rivets.