Is this a commercial dvd? Does it have encryption in other words?
You can rip to the hard drive with DVDShrink and get one big vob file by changing the Preferences to No Splitting into 1gb chunks. DVDShrink will only work on commercial dvds that have minimal encryption…the original CSS type. It is possible to select the main movie as the only output by going to ReAuthor Mode.
You can also use VobMerge to combine the vob files you have on the hard drive now…or Vob2Mpg to make them all one big mpeg file if that would work for you.
I don’t use CloneDVD, so I’ll let someone else address using it.