Need to compress/edit 2 badly joined MPEGS

I have two badly joined MPEGS JAV files that only Media PLayer classic can really read. But are slightly less than 2 hours long but most progs see them as either 29 minutes or 13 minutes or something like that. What I am trying to file is a program that will allow me to fix the files so that other progs can play/convert them.

What I really want to do is convert the files to REAL MEDIA so that I can burn them to CD-ROM