I just played through Zelda for the first time on PJ 64 myself. Those are documented problems. Open Project 64 (1.5 version, i assume, with the service pack), and click help, then game faq's. Click "games" then ocarina of time. It talks about known game issues and workarounds. And do get GoodN64 to check your roms. Info on that's in the manual for project 64.