If you have the full Muzzy stainless headers, I do not see why the other cans wouldn't fit. Muzzy's doesn't make different headers to match the pipes; that wouldn't make any sense.
As for sound, I think they do sound a bit different between canisters. I had a Muzzy SS one for my ZX-6. I have a carbon fiber one on my ZX-7R. I can hear a difference on them. How much of a difference? Probably neglible.
If you have any doubts about pipe fitment, call Muzzy's and ask them.
www.muzzys.com
PS: How bad is the scratch on your SS pipe? Have you tried to take the scratches out? I believe is you use fine grit steel wool it will take mild scratches out.
Stone