Hi, I found this thread N64 Save File Convert while looking for a way to convert my PJ64 saves to something that the Mupen64+ core would like. So after looking at it, and it being somewhat old and without a proper release I decided to write another one, while taking into account the actual mupen64 core save code.
The repository is here.
I used it with my save collection and it worked pretty well (with saves from 2006!).