Even with all the warnings turned off it will still turn off if it gets over 80C (75 for Intel, 80 for AMD). I'd get a temperature monitor off the internet (I recommend MBM5) and see what temps your case/cpu are at. If they are fine (~50C for an Athlon, 40 for a Intel) then no point in getting a CPU Cooler, If it's the HDD that's suffering from heat problems. You can get 5 1/4" Bay HDD coolers, it'd be worth getting one. As for the desktop fan and open case, this may actually worsen the heat problem - Most cases are designed to cool through airflow, and having the side off stops the airflow, and in turn increases temperatures.
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