Uhm. Does the itch app store saves in the cloud like steam does? while that would of course be nice, I doubt it can do that.
Do you want to reinstall windows or do you want to wipe your hard disk? As far as I remember you can just shove windows over windows - it is over 10 years since I installed a windows...
There is no such thing as mysterious programs stealing your ressources (unless you have a root kit malware).
Open your taskmanager and have a look for bottlenecks. You can see what ressources are used by wich programs. If you run out of memory, you will find the culprit. If it is cpu time, it is a bit harder, but you will see things doing things when they should not. And if it is boot time ... you have a laptop, why are you booting, that is what energy saving modes are for.
Number one ressource hoggers are 3rd party malware scanners. Maybe you have an now unneeded database installed, but that would not take active ressources.
Anyways, you should make a backup before.
And save games are sometimes in game folders, sometimes in user folder, sometimes even in the regestry. And if you have drm from certain games, that might get wiped accidentally too. But the type of game you get from itch are not installed in the classicals way most of the time. So they should reside in whatever game folder you unzipped them to. Unless you wipe your disk, they should be still there.