MBP hangs for 30 seconds and I've tried everything

I have been trying to fix my girlfriends laptop by going through the forums but I have reached a dead end.
She said that one day, she put her mbp to sleep and when she took it out later, it was overheating and still awake, with iTunes open. Since then, the computer will hang for 30 seconds every minute or two, depending on how demanding you use the apps.
During a hang, Activity Monitor shows no spikes in CPU, memory or Disk Usage, the mouse moves and becomes a beach ball if you click a bunch, and happens with any App, including Finder. When using Chrome, Mac asks if you would like to "kill the page" or "wait" which only shows for a few seconds before eveything returns to normal again (about 30s).
Things I have tried:
Sleep, Restart, Shutdown
Disk / Permissions Repairs (Disk OK, Permissions show "harmless" things according to the forums)
SMC/PRAM Resets, System Diagnostics
Lion Clean Install, Mavericks Clean install, booting from Recovery HD and a USB
Dusting the inside of the laptop, refitting RAM, physically detaching the battery
After all this, the issue still exists. Booting from the Recovery HD and USB I still experienced the hangs, so that led me to believe that the issue can't be the hard drive. I also heard that CPUs have protective mechanisms to keep themselves, and if RAM or video cards fail you won't be able to see anything.
If you have any ideas as to what could be the problem, please let me know. Thanks.

I also wanted to mention the hangs would also occur during OSX installations, and processes such as booting, shutting down, Disk Repairs and Permissions Repairs or OSX Reinstallation took 10-20x longer than estimated by the process (for ex. if it says 3 hours remaining It could take 24 hours to complete)
I will bring in the laptop soon to a Genius Bar, but I need to have the computer on me for the next week and don't want to pay a bunch of money to get it fixed just yet, since it's not covered by warranty.

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