The honest quick solution is to keep all important documents on a USB key and wipe everything for a clean install. What has happened sounds messy and long term it will be better to start fresh. This doesn't take long and will pay off.
Otherwise, put the key documents of your HDD on a key and wipe that.
For the SSD, go and deinstall big programms. Run CC cleaner, malwarebytes etc to clean it from a health perspective and keep using it.
An analogy...You have two carpets full of sand. You can either pick up what you want to keep and just thrash them and shake them clean
Or
you can take a fine comb and start sifting through and picking out stuff to throw away, leaving the rest untouched...
I know what I would do here...