Tom,
First of all, as I said, we RTM'ed the new version of IDU just this past Friday. It will take a day or two for things to trickle down and the files ot actually appear on download center. You are ok with 3.2.4 for now; watch for 3.2.6 to be posted and use it once it is...
Second, the stock heatsink-fan unit's fan pushes air down, through the heatsink and then out in all directions along the surface of the motherboard. This is the optimal airflow pattern. I have seen tower heatpipe solutions that have their cooling fins aligned so that they deflect some of the air down onto the motherboard. One of the places on the motherboard that we monitor is one of the major VR hotspots (we put a thermal diode as close to there as we can (barring routing issues)). If you are seeing the temperature for this sensor staying below 80, it's fine (though 70 would be better).
Seeming to run a little longer to lock up with the fans cranked up is not much of a proof of it being an overheating problem. You've got to watch the temperatures of everything that you can and watch for specific zones reaching levels that are concerning. If the temperatures are not rising to concerning levels, it's time to look at other possibilities. In a very significant number of the situations that I have analyzed, it has been the audio solution that ended up being the culprit. Most of the time it was the audio driver (why these are so often responsible for hangs, resets and BSODs, I am not sure). Now that I think about it, however, I remember a situation in which heat from the video card was affecting the audio card beside it. Hhmmm, you said you disabled the onboard audio and used an add-in card? Can you move this card any further away from the video card? If not, maybe you should pull this card for a while and use onboard audio and see if this positively affects the system's stability.
Another thing - the zone around the PCI connectors often get the least airflow. The front inlet fan is the one that best affects this zone. It's worth having this fan be the one running faster. Another way to loook at it is overall acoustics. The CPU and GPU fans are typically the worst. In both cases, however, providing them with cooler air to work with means they don't have to work as hard (spin as fast) to provide the same cooling benefit. Bottom line, speeding up the inlet fans especially (but speeding up the outlet fans helps as well) will often result in a reduction in overall acoustics. Think about it...
...S