The biggest challenge with that conversion is both Rolling Thunder and Genpei use a crap-ton of 28-pin 1Mbit mask ROMs. You can't physically fit the EPROM equivalent 27c301s into the 28-pin sockets. You would need to come up with some sort of adapter PCB to fit into these sockets. Theoretically yes it can be done. Also there are some customs that are unique to each game you would have to find a way to patch the game ROM.
