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I have the main drive replaced with a 10K 300gb WD Raptor also.

Perhaps thats the problem...

What is a good fan control app for me to check that as the noise source? It is very high pitch, so I don't believe its a dying case fan or power supply.
 
I have a 2008 MP 3,1 with 2 x 2.8 GHz - it is almost completely silent with 2 HDD (WD Caviar Black) and two SSD. Sounds like you may have a failing component. Have you tried taking of the side cover to identify the source?
 
I have the main drive replaced with a 10K 300gb WD Raptor also.

Perhaps thats the problem...

Could be, but I have 2 WD Velociraptors running in my MP 3.1, no noise to speak of .
Make sure the drives are installed and screwed into the drive carriers properly, I also squeazed some foam between drives and carrier handles .
 
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