I'm sure there is a way to do it, but I don't think I'll be the one to figure it out. There are also people who know more than I do about this kind of thing who have looked at Wind Waker and weren't successful at getting it to run at 60fps. After all, Luigi's Mansion does a frame rate change, and all that got me was double speed when I forced it to stay at 60. Even if I could make it stay at 60fps by changing a 02 into a 01, it likely would make the game run at double speed.
I actually don't really know how to see what Wind Waker is doing when it boots up. In the case of Mario Kart Wii and Metroid, it was simply a frame rate cap that I disabled, and it was a relatively simple process to figure out how to do that. I would love to get Wind Waker running at 60fps, but I'm pretty sure it is something more difficult than I could do.