Project64 is reasonably fast but does not have a lot of speed to sacrifice to highly CPU-intensive processes, like pretty much every emulator. Also, if you think that's fast, you should try 1964.
There isn't a way to just modify a ROM file like that, unless you want to enter the programming arena. If you want to make screenshots for your model modifications, export this geometry using a graphics plugin supplied by Nemu64. Check the Nemu64 forum for a sticky on how to use this feature.