[Y_Less]

All the suggestions are generally, do what you already plan to do. Make sure your interfaces are clean too - keep all variables "static" from the start and let different files interact with each other only through functions, that way you will find that modifying how things work becomes much simpler.

Also, look up y_master if you are concerned about code theft. That allows you to split your separate files up and compile them as filterscripts, so your developers don't have all your source code; but allows you to compile everything in to one single mode with no modifications.