Skip down to the "LONG STORY SHORT" if you're not interested in the Dr. House-like long version.
LONG STORY LONG
My computer was crashing under heavy load, presenting a number of different symptoms. There was no artifacting of any kind. Either the system would hang and I would hear the last second or two of sound loop over and over until I hard-reset, or the screen would go black while I could still hear the system and even interact with it (audibly). Playing games with my case open and a window fan blowing onto the motherboard seemed to increase stability. My first thought was that it was obviously an overheating issue, so I ran prime95 with speedfan open. I knew it couldn't be my videocard because I have an aftermarket fan that keeps it at a chilly 38c under load (no joke), because the stock cooling solution IDLED at a sweltering ~80c (also not a joke!). My CPU on the other hand, was loading above 60c, which made that the immediate worry. I lapped the hsf and applied new paste, but it didn't drop the average temps but 2-3c.
My computer then started doing this on the first boot of the day, after being completely switched off for the night, so I got into the habit of loading speedfan on startup. When I noticed it would happen completely without provocation, and when all temps, including the CPU temp, were well within safe limits. So, from this point I figured it was either a power issue or possibly bad ram. As I was switching out RAM modules for load testing, I noticed something odd. I felt a draft, and realized one of my 2 rear case fans was blowing inwards. I realized it had been that way for the 4 years I've owned the case, and when I fixed it so both fans were blowing out, my cpu load temps dropped 16C. I thought that was really interesting. So I thought "Great! All my problems should be fixed!". My computer seemed to run stably for 2-3 days, then it started crashing hard again. I seriously felt like I was in an episode of house for computers! I cured my computer with a solution that made perfect sense, and it got worse! It was happening more consistently with heat issues again, it was more prone to hanging/freezing immediately after windows loaded, after it had already done so once. Then I noticed something interesting. In speedfan, the "temp2" reading under load ran at about 50c, but the icon showed a green check. I figured maybe that that was my northbridge, and that speedfan didn't know that this may not be a safe temp.
LONG STORY SHORT
I removed everything from my motherboard, and subsequently the motherboard from the case to remove the northbridge hsf anchors from the back of the mainboard. I had NO idea getting that thing off would be such a pain in the ass. I tried wrenching that thing around for a good 20 minutes. I eventually locked a pair of vicegrips around it and tried wiggling it back and forth to loosen it up, but it wouldn't budge more than a degree of rotation. I smacked my forehead and cursed myself for trying so hard to wrench it free on a cold board, so I plugged it back into the power supply and ran it dry for about 20 minutes, then it only took about 3-5 minutes of wiggling to get it off there. After getting everything back together and tidying up the wiring, which I'd wanted to do for some time, I was excited to be able to compute without being at the mercy of the freeze demons. That was the solution after all. The temp2 readings reported a 15c drop in load temps for the northbridge, and my computer has been running free of hangs ever since.
All is not well though. After I put my computer back together, only 1 of my PCI slots work (PCI slot 4). I need at least 2 of the accessible 4 (1 is blocked by my videocard's hsf) to work so I can use my soundcard and my wireless card. Please keep all "just buy a new motherboard/system" comments to yourselves. I'm well aware that's the easiest option, but these are trying economic times. I'm worried I snapped one of the microscopic connections from the PCI bus to the northbridge, or at the very least smudged it with as5 causing a short. I cracked it open again and I did find a few smudges on the side of the chipset, so I cleaned those up, but PCI slots 1-3 still aren't working.
Anyone have any ideas what I should be looking for, or in what specific area of my motherboard? Is it possible that 1, possibly 2, of my pci slots could still be functional but not the other 3? It's also worth noting that all PCI ports are still providing power to the devices, but the bios and windows aren't recognizing them in any pci port but 4.
Didn't I hear a House ad during the Cowboys' game yesterday where he picks up the phone in bed and says "It's 7am - someone better be dead." I notice the "long story short" is about as long as the long version!
One thing you mentioned was re-lapping the CPU - any chance you used metallic compound and you dribbled some shorting out something?
Clearly, anything using pliers, hammers, chisels or acetylene torches on the motherboard can result in components getting damaged. And the motherboard is at least 4 yrs old, so any component can just "go" at any time. Those smudges you mention could have shorted something - removing the fried squirrel from the high-tension lines outside won't bring your toaster back to life.
Generally, PCI slots are combined with several "on-board" services, such as built-in network adapters, and controlled by 2 or more controllers. This is why you might see a 1394 connector being shown as being on Slot 7 even though you only have 4 physical slots. I'm not up on all the engineering but it's quite possible to "lose" several slots and still have a single slot associated with the unseen slots still working.
Some close examination of the System hardware items may reveal info on this. See what you have listed in the way of controllers and see if any show disabled or otherwise not working. Of course, without looking prior to the fault, it just may not list them. Clearly, you should have known you'd one day have this error and taken good notes!
Some pictures of you with the vise-grips working on the heat-shield would have filled out the story nicely.