autocheck autochk * is the correct value.
If the dirty bit was the only problem, you can turn it off per microsofts instructions: https://support.microsoft.com/fi-fi/help/160963/chkntfs-exe-what-you-can-use-it-for
Erasing of restore points is actually fairly easy. All you have to do is shut system restore off and they will all be gone when you turn it back on. Perhaps something in the process you went through did that.
You might try downloading and running Windows Repair All-in-one. It isn't a repair install, but it will correct some of the important registry entries in windows.