After careful consideration and after giving up the idea of doing something manually, I've opted for creating a bot that will go through all the code and will detect all branches and artificially run through them.
As a starting point I will use the tables that I have created with ElSemi's special version and MAME and I will do the following:
* analyse the game code and search for all conditiional jumps that are in the parts of the memory that we already know that's code.
* search if both possibilities have happened (jump/no jump). If any is missing, launch a subroutine that will follow that second branch line by line, jump by jump.
* search next conditional jump unit end of Code RAM.
I'm going 10 days off, so don't expect any updates in that time.