I rewrote my program, it doesn't need makerom anymore. It should be much more faster now and, hopefully, resolve memory issues. I don't have much time to test it right now so any feedback highly appreciated.
It doesn't work in all your games? Are you sure game you converted have manual? Many early games don't have it. I only tested few and manual worked fine for me... need more feedback.
you implemented the functionality of makerom yourself in your program? very cool