I have no idea which files CloneDVD needs in order to begin processing.
It seems to me you now know.

The main movie files, + the bup of the main movie set + the video_ts.ifo/bup files.

So just select those additional 3 files manually when you rip, or rip all the files as suggested earlier.

Even if the resulting dvd doesnt contain all of the additional stuff, it doesnt harm to include it in the ripped version on your hdd. You'll just have a couple more files to delete off your hdd once CloneDVD has done its stuff!