This is going to seem like a really, really dumb question, so forgive me in advance.
You DID take a can of air to everything, right? And really gotten in there and cleaned everything? Fans, connections, tops and bottoms, etc?
The only reason I ask is because I was having massive issues with my old jet engine. It got to the point where all her fans were going, and I had her side off and a big box fan blowing on her, and I was like, "Noooo, motherboard, don't die yet, we can't afford a new computerrrrrr" Then one day I had an epiphany and went to Best Buy and bought two cans of air, and went crazy. And then suddenly she ran like new and had no problems. And I put her back together again.
I'm sure you've done this. Just offering my idiot two cents.