While you've got the case open, take a good look over the capacitors. A common problem with motherboards, especially when heat has been an issue, is that one (or many) capacitors go bad, especially near the CPU.
All the cap's should be nice and flat on the top, no bulging and no corrosion/gunk built up. If any of them don't look perfectly flat, you have a bad/going bad cap.
Good news? You can replace a capacitor.
Bad news? Hope you soldering skills are up to par
Of course, looking for burn marks is also a good idea.
As for the hdd... Beastie has pretty much called it - clicking noises are a drive having a physical problem, typically a read/write head that is getting stuck. Backup (if you can) and replace ASAP.