Love the Ben Heck Bill Paxton effort, and his latest is a "Lost" themed game, which I'm keen to see too.

I think (no expert) you need the software tools that they made the ROM with to be able to recompile changed software. We built Coconut Island http://www.users.on.net/~spaners/Coconut%20Island/ from scratch and as was PC based, were not up against trying to make software compatible with old hardware.