Once the test has been "published" I don't believe there's currently an "un-publish" capability. You could probably modify the "Patron preamble" with a database query (I can probably help if necessary). You probably could also "un-publish" the test with the right query.
I'm not sure about test cloning, that actually sounds more like a bug than a server configuration issue. Is this something you're going to need to do a lot of?
The test/survey area is a part of the application that I am not super-experienced with due to running out of time to get all the improvements implemented that I'd hoped this year. It seems like it's mostly functional but I realize it does need a lot of improvement.