This is the route I came up with, can probably be optimized a bit, I need to confirm if a few things work that I'm wondering about. I came up with this as a different enough run from the original compared to the other MQ runs like any, no im/ww, and normal mst, which dont have that many differences. I know this'll never make it onto the leaderboards, but I hope this might inspire someone to put some kind of Master Quest run in there, it has a ton of unique routes to take, especially since 3DS MQ is more easily accessible than n64 MQ ever was.
P.S. Here's an MST route for Master Quest too, as an alternative if you like WWhttp://pastebin.com/f1RBuGZv