Some general observations and experiences.
1. I don't use SuperDuper so I cannot address your specifics, but like most cloning software, you start up from the clone, open your cloning software and begin a restore process.
2. In Apple Mail you can export individual e-mails or mailboxes. Export them somewhere and then import them once you have fixed your problem. You could also forward the new e-mails to yourself at some other e-mail address and retrieve them later.
3. I would think so. As long as you don't create a new clone on the SD drive, the state of that clone should not change.
4. The one time I worked with someone who did a Mail restore from Time Machine, it was very tedious. I was not involved in the Restore from Time Machine process, so I don't know what they did, right or wrong; I was called in afterwards to clean up the mess. Mail stores the e-mail, etc. in cryptic folders, beginning with the V folders you mentioned above. There are folders nested within folders within folders within… . Nothing is too obvious until you hit the actual e-mails, which you can then drag into your In Box. The process is better than not having them at all. And perhaps if the entire Mail folder in the User's Library is restored, you won't have the problem I experienced. Thinking out loud, it might be worth a try to use Time Machine first on the Mail folder. In a sense, you have nothing to lose.
5. If Time Machine backed up the Library when it was invisible, it will be there, but it is only the Mail folder in the Library that you want to restore, not the entire User Library.
