I'd wager that using that old version of the program gives you lots of trouble, yet starting from scratch may give you just as many. Maybe it's time to give an end to this story that you deem passable, and use a new engine to work on a different project? We love this game (I do, at least), but you seem chained to it, in a way. If it hurts you, and the idea of working on it gives you headaches, do consider what I commented.
Either way, I want to remind you that whatever you may choose will be fine with us, and we'll keep on fapping to what you already made (and will make!). ♥