I know my situation is not quite the same, as I have an ERA FIA with a small-block in it, but, what I did to fix this issue on my own car was to open up the holes in the body.
I could see witness marks on the pipes where they were hitting. I drew outlines on the body with a grease pencil, and trimmed the holes to give me about 3/4" clearance top and bottom. I used an air saw, and finished the rough edge with Dremel tootsie rolls, then touched the raw edges up with brush-on touch-up paint.
I actually did this twice - the first time with the side pipes still on the car. Naturally, it was a little difficult working around the pipes while they are still protruding through the hole. The next time, I took the sidepipes completely off (I do that anyway about every third year, to respray the side pipes with VHT White paint). I know it's not an elegant solution (do I mess up my $800 ceramic coating? or my $10,000 paint job?), but, the witness marks on the pipes were really bothering me. I hardly notice the holes in the body being larger.
regards,
Jeff