Jessman,
I have a modified Glide3x wrapper build here that might help with the speed problems associated with Perfect Dark in Glide64. Essentially, the texture generation code is rewritten, which helps with framebuffer generation as well. Also, other performance tweaks were made as well, and I fixed that typo in the config in update 9 of the official wrapper. I only really extensively tested these optimizations with Perfect Dark, Legend of Zelda: Majora's Mask, Blast Corps, Paper Mario, Banjo Kazooie, Sin and Punishment, and Super Smash Bros.
Hope this helps.