There is no way to work around the TOC limit. And the options for making your backup playable are limited. Go to
http://www.spiv.de/ps2 ... there are patches called "no-mod" which reduce the size of the games. Or, you could extract the files from your .iso and dummy or downsample a movie file to make the size 640 or under, then re-create the iso and you're good to go. The 'no-mod' patch is obviously the easiest way to go and probably what you should look into first.