basically if you have one of the clones which is acting purrrrrrfect and you double check that you havent made some data files since the last cloning etc that you need
then YES select full back-up and then you will have an exact duplicate copy of your "better" OS
I would advise though as a saftey precaution that you download and use Driveimage (see my links) to make a copy of the drive you have with "shell" problem just in case things dont go as we expect. In that event you could use the image program to return it to the way it was >>>>> pick a drive that has plenty of empty space to hold the image file as it will be approximately one half the size of the OS drive you want to "protect & back-up" if things go as I think they will, and a week or so goes by without a tragedy, then you could either save the image file forever, of delete it.
Its easy to play with things when you know you can revert back to the way it was.
I wish I had a Image program for my life
but I could settle for an authentic
Easy Button (not the staples one either!)