I am running macOS 10.11. The system is as far as I know not infected, but natural I can not be sure. The system was in the past not as secure as it should have been (missing security updates and suchlike).
I want to use the opportunity of the update to 10.12 for a fresh and safer restart. I am going to make a clean install. Of course I have to copy my files to the new system. I fear that copying my old files will compromise my attempt to have a secure restart. I fear copying bad things to the new system. I will have to copy all my documents and media to the new system. Because of my very slow internet connection I also think about copying programs from the backup instead of downloading everything.
Am I too paranoid? What can I do to make it less likely that my new system is getting compromised by the files of the old system?