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Did you also clean the heatsink? You may have blown all of the dust bunnies from the fan deeper into the heatsink or the intake ports.
You should consider taking a vacuum to intake and exhaust ports. If that doesn't work, open it up, take out the heatsink and clean it, and apply new thermal...
The Apex PSU runs really hot is isn't all that good... If and when the PSU does die, replace it with a Seasonic unit.
I used to have the same case along with a Intel D945GCLF2 motherboard and replaced the original power supply with a Seasonic SS-200SFD that I found on ebay for $18.
Has anybody updated their BIOS with the one that iDOT currently has?
http://www.idot.com.tw/en/downloads/MB-PC2500E(ID-PCM7E_v1.0C)/831BIOS.zip
I'm afraid of updating my BIOS, due to the fact that the motherboard in manual looks different than the one that I have.