All you should need to do is pop the cover to dust it out. Which is not a bad idea to do every couple of years.
But, I'm not sure thats the root issue here.
Sounds like some application is hogging the CPU and HD resources causing the heat buildup (which over time will kill your system).
Rename the back up'ed removable HD system folder so it's not used. Then install a new copy of system files on to the removable HD from the OS-X install CD/DVD's so you have a straight vanilla OS to boot from. Using the Startup System Pref select the removable HD's fresh system to boot from.
Once you get there let the system run as it would when you encountered the HD noise and/or noted the heat build up. Is it still doing it? If not you have something running thats killing your system not a dust buildup problem (still could be a HD on the way South though).
Using a good copy of anti-virus software you can check to see if you have some malicious software running (Malware). You could also have background apps like antivirus, antispam, Peer to Peer or application pre-loaders (MS has a few) that are mis-behaving. Make sure you've upgraded all of your primary apps and removed any that you won't be using any longer.
You can also use the Activity Monitor app to monitor whats running click on %CPU column to see whats the killer (using the internal HD to boot from). WARNING: Quitting a process can make your system unstable so make sure you don't have any file open that you can't replace. Comparing a clean install Vs your running system can help you in isolating the normally running Apple OS processes as ones not to touch.
Also check network activity in case your system got zombie'd by some malware that for some reason has kicked in. Nothing should be going across the net (constantly) unless you're accessing it from within an app.