Unfortunatley I find Mupen too unfriendly to work on and I would only be prepared to do it as part of a team, but I would be more than happy to be the front runner of it all, if you need to hex edit the best thing you can do is open two Mupens at once and use frame advance on the old version so you can copy it, although the randomizations and slightly different camera angles could render almost useless. I've been figuring out the perfect ruppee route and it may be possible to do it in 1:50 with a speedrunner doing it in 2:01 with uber luck. The bombchu ocarina trick (with sword of course) would save about 8-10 seconds and yes it does require a fish and the bottle to be present in Links hand.
http://www.youtube.com/watch?v=g0_XkFqmIm8
Here's a detailed comment someone gave on it
Get a bottle, then catch something in it (fish is easiest). Go somewhere you'll need the Ocarina, let the fish loose and re-catch it (this makes Link hold the Bottle in his hands). Do a backflip/jump from a ledge, and while in the air, press the Bottle C-button and then another C-button with an item (or even your sword). Link will pull out the item and put it up to his mouth, working as a fully playable Ocarina.
