Re-encoding Archival Movies
For such low quality footage (320 by 240 was quarter resolution even in the early 2000s), I'd probably go with DV format.  It's a major video standard that, while not used much anymore (though HDV is still used), was a major video standard and thus isn't going anywhere quickly (just look at how MPEG-1 has hung around).  It is designed for high quality video in SD formats and was one of the most common standards for that type of video even at the time of your project.

Many of the MJPEG formats were a pain even when they were new.  I know I had issues with my Matrox MJPEG format content not working without some level of difficulty even when it was current.  DV on the other hand, I've never had a problem with anywhere, including current systems.