Now to find out how to do frame-by-frame inputs...**GAARGH DAMN PAUSE BUG GAARGH** dammit.
That's a hotkey that you press on the keyboard like RG said, and you need a specific version of Mupen64 that has the pause bug fixed. (Just search "Mupen64 re-recording OoT edition" and you'll find what you need.)
SL has another way of fixing the pause bug for the reset recording version but he hasn't given me the details on what to do.