I've heard that one approach to these kinds of projects (small number of games, no original source code) is to translate the code to (really ugly) C and compile that into a library-like blob; this can require manual intervention for runtime-dispatched jumps, overlays/mappers, and other dynamic oddities. At that point you can start using host/target debugging tools and it's "just" a matter of finding the entry points and data structures that you care about (player inputs, graphics patterns/palettes/coordinates, timers, etc.) instead of trying to RE the entire ball of mud.

Come to think of it, I think I remember reading about someone that did that with some DOS-era games to port them to ARM handheld game systems. I've got a similar target in mind. I've played with manually translating some of the assembly listings to C. Maybe I ought to continue going down that road, or seeing if some previous work has made some tools to help automate it.