well, just follow the help instruction to use suggested plugins.
Jabo D3D video plugin 1.2 or 1.3
Azimer Audio plugin 0.30(old)
Nrage input plugin or some other input plugins.
You should at least get Super Mario work.
Try to read help more closely before asking more questions. You should do it because most of your questions should already be answered in either 1964 help page or PJ64 help page.
Please also see Smiff's page at:
www.smiff.clara.net
He has a lot of help information.