First, you need a fan. If your CPU gets hot, you will have those problems. I have a fan on my CPU and on my hdd.
Second. Clicking is your hdd on the way out. Just because it doesn't register any problems when booting up doesn't mean it is okay. Does it do it all the time? Run a diagnostic program from your hdd manufacturer's web site. They are usually free.
An hdd can be on the way out and still be working. When it hits the sectors that are bad, you get the clicking. Been there a few times! That is why I have a few extra hdds.