Since your temps seem okay, and your USB ports intermittently crap out, then it's not unlikely that your motherboard could be the problem.
The next thing I would check before the motherboard, however, is your power supply. If your power supply is on the fritz or if it's just giving enough juice to run your computer and little else, then weird things like your USB ports malfunctioning can happen (especially if you're using a bus-powered device like some external hard drives). The moment something draws more power than your power supply can muster, your PC will shut down.
So if you have a spare power supply that's decent, try that out.