EEPROM and Mempak saves should be easy to convert, or can be used w/o converting but may need to rename the file.
You can compare the PJ64 save filename and 1964 save filename, and you should be able to find the filename difference and tell how to rename them.
State save files may be convertable if someone like to write a small utility to do it. Since 1964 0.6.4 source code is released and PJ64 state save format is known, someone should be able to do it.