Something just coming to mind now is if I remove the exits section from the aircraft.CFG will it work.
That would be a sure way to have everything stop working, instead. If you can operate all the doors, assuming you made a correct GSX configuration for the merged configuration, it should work.
Another thing you can try, is to name the airplane folder in an entirely different way, such as CS_B767-300_LevelD_Merged. This way, there wouldn't be any chance for GSX to assume that airplane is either the CS or the Level-D 767, but an entirely new model. Of course, you will still have to create a custom GSX config for it.
This because GSX also uses "Pushback constraints", which changes depending on the airplane. For example, on the CS 767, you must also remove wheel chocks, engine covers and all the other stuff before allowing pushback to start. Perhaps you turned off all GSX warnings (something we always suggest NOT to do...), so you are not seeing that GSX is expecting those constraints to be solved too.