Don't worry, guys, I'm gonna submit v2.02 sometime tonight so you can just apply the whole thing to a clean ROM!
Edit - Would anyone like to wait on v2.02 so I can release some supplements along with it? I'd include an item list, an equipment list, a magic list, a shopping list, and a magic acquisition list. Basically, all the cool little "feelies" to make it seem more like a deluxe release. There would be spoilers, but I get the feeling that many people who play Project II: FFIV have played the game before.