So, to be clear: the arcade ROM is distributed as a bunch of files, and you modified one named pzf.04, right?
So, all you need to do to make an IPS file is to get a program like Lunar IPS. Direct the program to the unmodified pzf.04, and then to your modified pzf.04, and it will make an IPS patch that people can apply to pzf.04 obtained from elsewhere. Does that make sense?
(Such a pity they never released the HD Remix on Steam.)