It sounds like you have an “interesting” situation with your computer in the sense of the old Chinese curse “May you live in interesting times.”
You have so many things going on that I can’t give any firm answers but I’ll touch on a few points.
The thing about proper air flow applies IF the case is closed. Leaving the cover off actually is a solution to air flow problems but with three case fans, rounded cables, and an 80° case temperature that doesn’t seem to be your problem. It is also easy to spot non-working fans with the cover off.
BIOS flashing is probably my least favorite thing to do on a computer. I’ve never come across an explanation for why sometimes it takes on the first try and sometimes I have to do the very same thing over and over again until it works. The only thing I can offer there is to be sure you’ve completely removed the old BIOS. It’s motherboard specific so you’ll have to do some research but you need to remove the motherboard battery and locate a specific jumper that drains the BIOS.
Yes, Arctic Silver probably is the best thermal compound and I have some myself, but I really think it’s overkill unless a person is pushing a system to it’s limits. I mentioned the Radio Shack stuff because it’s probably quicker to go to a local store and try it out than to order from a website and wait and pay shipping ... and the stuff really is good enough.
Reseating the heat sink is no big deal. The first time will take a while but after you’ve done it once it only takes a couple minutes. I’m pretty sure you can find very specific instructions if you dig around on the Asus website. It is entirely possible that the seal has broken; it only takes a slight twist of the unit, frequently caused by poking around in the case while routing cables or such. The Thermalright heatsinks are extremely easy to install; no soldering, just clips on.
Prime95 is a favorite for stress testing. If you computer will run the torture test for a while without overheating or crashing, well ... have fun. It sounds interesting. [img]/images/graemlins/wink.gif[/img]