Try to play around with the counter level setting, I have heard it's similar to Frame Skip, except it approaches the problem in a different way.
On to topic, use 1964 (Make sure you use the no sound plugin), its about 30% faster than PJ64 but you probably will still experience some slow downs. If you want full speed, use the no sound plugin - it increases the frame rate by a fair bit, the downside is obvious: you won't get any sound.