No..the disk Clean-up is part of the OS for Windows, it should never harm any of your other files or programs. It just gets rid of assorted files that have accumulated during the past few sessions from your computer. It compresses files after you've checked if you want them done in 1-100 days.
You could also do a disk defrag on your computer to see if your computer is fragmented-sometimes if it is badly fragmented it will run slowly and work harder than it should.
If the Clean Installer is not in your listed Programs, that means you do not have it on your computer. I don't know why it would list out if you do have it, unless there are some scattered files left on your last install.
If this doesn't help, I don't really know what else you can do, except perhaps a registry clean. That one you have to have a separate program for, and there are a few free ones out for download-one I use is "Eusing Free Registry Cleaner":http://www.eusing.com/free_registry_cleaner/registry_cleaner.htm
It does a great job and does not take up a lot of space.