Either switch to 1964 which is faster, or greatly decrease the screen resolution in PJ64. The Glide plugin is very fast so you might not need to switch to UltraHLE 2064, but you might have to if 1964 is too slow.
The manual for PJ64 says that an Intel Pentium 3 700Mhz or AMD Athlon 800Mhz CPU is the recommended minimum, so that's why it's slow.