If the only reason you're not using h2xs is because it creates new files (blowing away the ones you already have), then the solution might be easy. Copy your .xs, etc. files into a new, safe location, and run h2xs on them there, to generate a sample Makefile.PL. Then steal the clues from that Makefile.PL, and paste them into your hand-built Makefile.PL.

Of course, I say this not understanding your file/directory structure: it may be too complicated to get completely useful results. But perhaps you could pull out just enough of your code to give h2xs the clues it needs to help you?

Alan