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I think Spacefrog is right with the exhaust fan. I ran smcfancontrol as bearcatrp suggested and the sound goes away when I speed up the exhaust fan. Looks like this is what I'll be replacing!
 
Update: So now my 3rd HDD is back in and it really seems as if the noise is coming from the PSU. I sped up the exhaust fan and took the panel off to listen, and it was not coming from there. After taking a closer listen to the PSU, the hum is definitely coming from there, and it also sounds as if the fan is grinding inside. Does this mean the fan is causing all the noise? How would I go about troubleshooting this or even replacing it?
 
Update: So now my 3rd HDD is back in and it really seems as if the noise is coming from the PSU. I sped up the exhaust fan and took the panel off to listen, and it was not coming from there. After taking a closer listen to the PSU, the hum is definitely coming from there, and it also sounds as if the fan is grinding inside. Does this mean the fan is causing all the noise? How would I go about troubleshooting this or even replacing it?
Pull the PSU from the system, and open it up. Carefully, as you don't want to touch the capacitors (they will still have a charge, and can zap you). Remove the fan and replace it. You may be able to unplug it, or you may have to use some other means (desolder/solder in a new one, cut & splice wires via soldering + heatshrink tubing, crimp connectors, or even wire nuts) assuming it's soldered to the board.

I've not been inside a MP's PSU, so I don't know how the fan's wiring is connected. But overall, it shouldn't be that difficult. :)
 
Unless smcfancontrol has been updated, it never was able to spin up the PSU fan. If it does, can you tell me what version your using so I can check mine again?
 
vacuum the inside of it. the fans might get stuck with lint and dust.
 
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