Can you boot into safe mode?
If the microdrive has been sitting for several hours, and then you turn it on, how long after does it crash? 15 minutes? 5 minutes? 30 seconds? How hot is the microdrive after 5 minutes? Mine would only really get hot after many (5+) hours of running with programs running. If it is just sitting there, the whole unit is still hot, but the microdrive seems just warm.
The reason I ask about safe mode, is my initial windows installation would always crash right after the windows screen came up. However, I could boot into safe mode but that was it. No matter what options I picked, the only way was to get rid of the ACPI stuff and use the fail safe bios detection thing.
Also, what I did when I was trying to OC it, I put a big house fan right behind the iaone, turned it on high and that really cooled the entire case and microdrive. You might try that to see if it makes any difference.