Why not just acquire all the flutes, then you can switch them through the pause menu.... but that IS a wonderful idea.

Dont ask me how to accomplish it though... I'm clueless.

I don't think the game will actually allow you to do this because of the designated few screens where depending on the animal you chose, changes. I'm pretty sure that even when you obtain another flute it just changes your other flute, not totally sure though.
All a gameshark code does is change one value in a memory bank/address into another, so in the end you're going to have to write a value to the flute address. The only problem is, it's going to be hell to write. The dialogue code is all over the place so it's kind of gonna be really hard. However, you can do something easier like making the flute obtainable in a chest and modify the chest loading code. You'd do something like checking the first chest value, and if it's xx, don't actually give you a weapon, but just modify the flute you have. Though, it'd be kind of hard when messing with dialogues, but you can place a check on those too. I don't know, but it should be more than possible.

Great, all I need to know for now is that its possible, thanks for your help.