The process was surprisingly smooth. I was prepared for all sorts of problems along the way, but it just worked. Uncanny...
I ran the TOP853 software from virtualbox to read the roms into .bin files and then i used bokken from the ubuntu repos to parse and look at the files. This is how I did it:
|Open the chip select dialog in TOP853.
|Type in 27256 and select EPROM.
|Select a long delay for reliable reading.
|Start reading the chip into the buffer.
|Save the buffer to .bin file.
|Open bokken and select the .bin file.
|You can browse the dis-assembled code.
|You can view the strings table.
Figuring out what to change in the code and where might seem harder than it is. I thought about ho to do it and I came up with the idea that the strings tell me something about what the code does, so all I have to do is to follow the strings and see which code pushes the strings around. Next I just identify which strings relate to which functions (such as loading/saving MSD data) and hijack those routines by jumping to an unused location where I have some space for my own code.
Well in theory at least.