Are you sure it wasn't self-bootable when you got it? MvC2 is a pretty recent game, not sure why you would find one that wasn't self-bootable. But this is besides the point.
You said your computer reads the disk as an audio cd. Have you looked at any other self-booting cd you've burned? This may not be true with everyone, but whenever I try to look at a game I've burned it only reads "Audio CD" and when I try to explore it it says please insert a CD. However, when I play it in my dreamcast it works fine. When I explore the tracks using DJ and compare them to the *.CDI image its a perfect match.
That said, I believe what you are trying to convert into a self-bootable is already self-bootable. Theres no reason to have an audio track on a non-self-bootable game. I've never even burned a Boot-disk to try it, so I'm not sure if a failed self-bootable will work with the Utopia boot-cd. I would assume it would if the data part isn't currupt. If it can't, ignore what I just said
If what you have IS a self-bootable, try using different methods of burning or just try again
