1000 things wrong does seem to be a lot for sure. Not only the OS updating things, but it also depends on how much software you install and more importantly how much one uninstalls, for crap is left behind in the registry. This is due to poorly written uninstall programs. I think it to be safe with CCleaner to fix the issues. Make sure you use the backup option if you do.
I don't know PC tool, but one must be careful of 3rd party maintenance programs. Most will damage the system more than help. CCleaner I find is good. I think most on the forum will agree.
I was in IE10 (desktop) the other day doing something (I can't remember what) and it crashed a few times, but recovered. It happens from time to time. Not a big thing really, just as long as it's not frequent.
Have you run the temp file cleaner side of CCleaner? How about virus scans and Defrag? Are those being performed regularly? Dskchk I see is automated in 8, but running that may not be a bad idea. It won't hurt.
Any issues in your Action Center?