Very nice monitor program there. That's a start for the temperature side of things, just in case.http://www.freedrweb.com/cureit/
Free virus scan. Also hunts for rootkits. Very handy. That's step #2http://www.malwarebytes.org/mbam.php
Step #3... checks for malware, scareware, etc etc etc. Free version.http://www.safer-networking.org/index2.html
Malware/spyare checked #2. Also contains a monitor for your system to guard against attacks, rather than just cleaning up after them. Also free. Works well with previous malwarebytes software... they don't fight each other. Nice combo.http://www.javacoolsoftware.com/spywareblaster.html
Free software to prevent your web browser from accessing known hostile sites. Works well in conjunction with Spybot S&D. Modifies the hosts file to prevent the sites from loading. Very handy. Free version must be manually updated (extremely easy) Pay version can be automated.http://free.avg.com/us-en/homepage
Free antiviral, includes a resident monitor for guarding against attacks, again, instead of just cleaning up after them. Not the best AV in the world, but it's free. If you have one you prefer, use it instead. Note that this does not preclude use of step #2 above, since that step also spots rootkits, etc. AVG doesn't. Warning: Annoying feature they added forces free users to install the AVG toolbar for Mozilla/etc. And that sets your default search to yahoo, which is doubly annoying. But at least it's free.http://www.piriform.com/ccleaner
Very handy little utility for keeping your hard drive all spiffy and clean. Purges old temp files, etc etc etc. Also free. Noting a pattern here?http://www.piriform.com/defraggler
A handy defrag utility if you don't like the windows version. Yep, free too.http://www.auslogics.com/en/software/disk-defrag/
A second free defrag utility. This one being the fastest defragger I've ever seen. I no longer use defraggler, unless I happen to be in the mood.
Oh yeah, last but not least. http://www.revouninstaller.com/revo_uninstaller_free_download.html Yep, free. A very good uninstaller program. Contains the ability to search through your drive/registry for bits that would otherwise be left behind by the regular uninstall routines. Very good for rooting out unwelcome software. Also contains a hunt feature for rooting out software that doesn't have an uninstaller/entry in the programs control panel.
I use every single one of these, and to great success, in keeping my machine squeaky clean. Some of them (spybot, avg) contain active monitors that run in the background. The others are ones you run when you get in the mood, and then put away.
Start with the temp monitor and the dr web cureit.. that will reveal hardware issues and extremely hostile software (rootkits, etc). Then just go down the list. If you need to uninstall stuff, get the revo uninstaller I listed last, and use that to remove stuff... be sure to let it do its scan... it will come back and ask you what you want to do with anything it finds.
I've yet to meet a system that couldn't be brought to heel with the above tools. Even my ex-managers personal system that was loaded with rootkits, virus, and malware galore. It wasn't pretty when I was done, but it was functional. And frankly, if it had been mine, I've have wiped it and reinstalled... it was that bad.
That said, your problem isn't one I'm confident can be solved with software... time will tell, I suppose.
PS: Ccleaner also has a registry cleaning function for clearing out orphaned/unused registry entries. Handy to run a pass with this, after uninstalling anything, just in case something got missed. Be sure to run the tool twice... the first pass will remove entries, which often creates a second set of entries that are now orphaned. Etc etc.
If you don't recognize something in your add/remove software listing, google is your buddy. You can track down all kinds of crap. Try by title, and if that doesn't work, try by filename ie 'unfriendlylookingprogram.exe'
Oh yeah, for your fan, just check and see if it's passing a good amount of air. If it is, you're probably covered. If the fan isn't running inside, generally speaking the restriction of the psu casing/innards, will cause air from your system to mostly exhaust through the back panel/video card vents/open hole and back out through the front, rather than through the psu. So if it isn't running, you'll get just a little bit of air through the psu, and frankly, it'll be extremely hot. If it's blowing, and it's warm, you're fine.