To those who are having desync problems, I managed to find the right combination of Mupen64 versions and plugins that made it sync up for me.
The 7zip version of Mupen64 from the mirror linked
in the Mupen64 thread didn't sync for me, despite having all of the plugins required. Link got as far as getting the Kokiri Sword, and then started slashing a fence repeatedly. The link for the installer version doesn't work.
However, I found the installer version linked on the SDA boards (
http://www.bluetoaster.net/emu/app/Mupen64%20v8.zip). Oddly enough, despite both of them technically being Mupen64 v0.5 Rerecording v8, they're different builds. The installer version seems to be the "right" one, since a) it has movie playback and record options listed in the menus while the 7zip version does not and b) it syncs the movie fine for me.
But, since the installer version doesn't have the TAS Input Plugin required to play this movie (at least, I think it's required), you'll need both versions--the 7zip download
does have it.
So, copy over the plugins you need (should only be the TAS Input Plugin) from the 7zip version to the installer version. Make sure you check the "MemPak" option in the Input Settings for Controller 1 and you should be good to go.