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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 .
 
I'm quite certain the Raptor is the source of your noise problems. Mac Pros are usually extremely quiet.

It is the problem. I have 2 of them that I removed. They raise the case temps so much that the fans run high constantly. Not to mention they're noisy all by themselves.
 
It is the problem. I have 2 of them that I removed. They raise the case temps so much that the fans run high constantly. Not to mention they're noisy all by themselves.


This sounds consistent with my experiences with Raptors. Heat and noise are the reason s why I shied away from them.
 
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