Well, this isn't good. I just started up Master Quest to start mapping it, but now I'm getting a "too many commands" error and the graphics aren't showing for the video plugin I use to rip the models. I know it was working last time I tried, so it probably has something to do with when I updated my video driver some months ago.
Edit: Very bad news. It isn't exporting textures or VRML data for the game, either. I'm going to have to either piece together all of the maps manually, or find another way to rip it. Otherwise, I may have to forego Master Quest.
Edit: Good news! I found an old VRML editor thing from 2007 that can actually open the weirdly-formed VMRL files created by PJ64. Sure, the model it spits out is squished in one direction and might not have the textures done properly, but this is better than nothing. Whether or not it works well enough for me to continue is something you'll find out in a day or so!