Just an FYI, the browser won't work with your M3. You need to have a DS Slot Flashcard to run the browser. You need an M3 or similar GBA slot card just to get it to load.
As for patching, the loader for my G6 has patching abilities, although I've never used it so I don't know if it can handle that file extension. Have you looked at your M3 loader program yet? You probably have, but figured I'd ask.