I answered to a similar question over a year ago here:
http://yabb.jriver.com/interact/index.php?topic=27464.0. The v.3.99 codec can read older versions, but it is not available for MJ8. You can use the separate Monkey's Audio program and MJ8 for converting the files to the previous Monkey's Audio format. The conversion process would be lossless. Check the link for more info.
The last MJ8 build was published in 2003. Since MJ8 was finalized JRiver has released five versions of their newer program, Media Center. MC supports the latest Monkey's Audio codec and probably will always do since the creator of Monkey's Audio works for JRiver.
I would suggest you to try MC. It has a 30-day try out period. Keep in mind that MJ8 is not compatible with MC anymore. You need to uninstall MJ8 first. However, you can make a library backup file with MJ8. The backup file can be restored in MC (and of course in MJ8 if you decide to continue with it).