Hi, GDT.
The best action would be to back up your computer, go through the cleaning process and then create a new, clean backup. If there are critical documents and pictures that you don't want to lose, it is also a good idea to back them up too. You can always copy them to OneDrive or DropBox. As to "must-retain files", if they are that critical, I suggest they be saved to off-line media such as USB, CD or DVD. In addition, although a system restore point is created as part of the cleanup process, it is always wise to create a fresh restore point before making changes to your computer, giving you a point of return. Thus, that is one more step you can take.
If you have any additional questions before posting the logs, please feel free to ask.