"How much of it would you guess needs to be modified to work with windows?"
I'm guessing just the input and output. If I get the source code, I'll port it to the cross-platform Allegro library. This will allow me to make a DOS version, a Linux version, a BeOS version, a Mac version, and a Windows version. And it'll use Allegro's decent file selector widget, so no more ctrl+L and then type entire path.

"I know it's a protected-mode program, does that make a difference?"
Depends on which extender it used. If we're lucky, then the source should compile with a bit of work in DJGPP (GCC for DOS), and from there, I can port it to run on top of the Allegro library.

I'd be willing to do the porting grunt work; I just don't feel confident in my negotiating skills. If Bananmos turns us down, I guess it'll be time to bite the proverbial bullet and migrate to a new music system.

"if migrating to incompatibe OSes can be considering 'upgrading'"
Old PCs break. New PCs purchased at retail often aren't very compatible with FreeDOS and DOS apps because DOS apps depend on specific hardware implementations of the input and output devices. When DirectX became more popular, manufacturers no longer felt the need to keep backward compatibility with DOS games.