I have the 3.3 pro, so maybe its difrent for 2.1 but heres my take.
The GS doesn't work unless there is a game attached to it. Thhats why just the GS wouldn't do anything.
OOT is also one of about 10 games that need to to activate a code to use it. You must first put in another N64 game (Starfox 64 for example), you then have to activate the zelda code, then turn it off, put
OOT in, then turn it back on.
Like I said, I'm using a more advanced and newer version, so what I'm saying may not be true for your version. If it makes you feel any better though, I have deleted several
OOT saves while trying to access the beta that is stored away on the gold cart, and have permantly ruined my copy of Super Mario 64 (It crashes every time you press the R button, since I was using a cheat that caused the collision detection to turn on and off when you hit R when the game got screwed up). For future referance, I suggest playing and beating the game normally before you try modding it, that way you aren't missing anything if it gets deleted.