You can leave the Proxy, CD/DVD and Sidebar repairs but I'd include Repair Important Windows Services - I don't know if that would default them but you can leave the 8/10 repairs, although it would ignore those anyway if you aren't using 8 or 10.
Before you run the program, I'd run a sfc /scannow and a chkdsk /f
The program can repair Permissions if it will let you run the program in Safe Mode with Networking - not sure about the Save though.
Have you tried your restore points, preferably in Safe Mode to see if that will resolve the Permissions and Save problems - these may have been caused by something you have downloaded, so an antimalware scan with something like the free version of MBAM probably wouldn't go amiss.
https://www.malwarebytes.com/mwb-download/