adding to the responses you already have . .
I would suggest you change the output size indicator to the left of the quality bar to "DVD+R DL" when ripping to your hard drive. That should change the percentage to "100%" - and you will not further compress the video during the first step of your process.
Then, open CloneDVD2 with the ripped files as your input, change the size indicator back to dvd-5, and peruse what you have, eliminating anything you do not really care about as a means to save space. Be careful about selecting audio tracks to keep to make sure you end up with what you want (ie. don't leave yourself with only a director's commentary or something like that) - and also subtitles (in case your film has some forced subtitles that jump on and off only when needed for certain scenes).
When you have unchecked the items you don't care about to save space, you can burn your backup. The program will run the transcoding routine if necessary - creating something to burn from in a temporary space, then burn from that space, and delete it when done (if you have checked the box telling it to delete the temporary space).