Okay, first of all, let me state that as far as I was aware, more or less the point of this roleplay was to have fun messing with a variety of universes and doing things different. It certainly isn't the combat, not with every PC being enormously powerful to start with for almost any standard, there's no fun to be had with stomping through everything with a straight face and no system of conflict resolution defined for it.This is my opinion, but while I'd keep things like chickens being unkillable canon because it's stupid and funny and would make the PCs that don't have meta knowledge crap themselves, I'd change the Master Sword being a Link-only thing entirely to see his face, as it were.

Having said that: The goddesses thing and the Master Sword's origin was created for Skyward Sword, a game released over a decade after the Ocarina of Time universe we are currently in. Twilight Princess Zelda says the Master Sword was made by the Sages, so the story for it isn't set in stone. Wind Waker claims the sword needs two sages to pray to the gods in order to keep its evil-repelling power, nowhere else is this mentioned. A Link to the Past doesn't specifically state Link needs to use it, only someone pure of heart and strong of body, could be arguably used to justify Bee not being able to take it, still nothing that states Link and Link alone can use it. 

There's little to no evidence that the sword can be wielded by Link and Link alone. In Skyward Sword the Goddesses chose Link, but who's to say they wouldn't have chosen somebody else if a better candidate was presented? Twilight Princess, again, says "only the true hero" can use it. I'd think multiversal avatars chosen to safeguard all of creation outrank Link in this department. Bee has solved the puzzles, his entire powerset is based around swords and the courage bit, well, I'd say it takes some courage to go stand up to the world-ending pig demon. We can also find new ways to break into the castle that don't involve the sages.