Make sure your computer has enough ventilation.
Also make sure that the computer is clean, has enough space to breath, fans are working at full capacity.
Look for anything that you arent using and try to lessen the power usage and of course try to make its environment colder.
You are obviously doing something wrong that isn't heat related. My guess is your BIOS needs updated as it is incorrectly reporting the system CPU temp. I had the same problem with a Shuttle PC i bought, so I recommend flashing the BIOS with the most current version, good luck!
i think HD usually generates less heat than the rest of components like cpu and gpu.
so if the HD is at 90c and u can still boot up, thats not really possible i think...
well, i dunno how much heat HD can take so i cant tell u for sure..
but im just generally thinkin that any HD cant operate in boiling water temp.
am i wrong?