Games that show up in your Library (meaning they are linked to your account) will still be there as long as you log back into your account. Games that are not linked (because they were a free download) can simply be redownloaded if the uploader has not removed them or anything like that.
For the save files, they are stored either within the game folder (like a folder named 'saves') or somewhere in your windows profile folder. It can be... difficult to find all save files for every game, as the store location and naming can vary greatly. So I would make sure to at least look up the ones you definitely want to keep and either upload them to your personal cloud (if you use one) or copy them to an external storage (like a sd card).
I do not think that your pc would have problems specifically of something in your personal files (at least not if it has not become infected with a virus or just is a total mess of files from over a decade). But in regards to windows I learned that, at least if it cannot be solved differently (by removing some programs for example), it is always best to make a fresh install to get rid of all problems the system has gotten over time. Any of the other methods may solve the problem, but there is a good chance that it does not or that some things will still be broken.
Hope that helps.