Dude, I had one of those MDD G4's and it was the primary fan that was at fault, by simply replacing it with another, it solved the entire issue with the noise. Actually Apple sent me a replacement, after calling and complaining a few times.

You might try that and see. Open it up and see if its that one fan causing the issue. Its the one blowing on the heatsink, IIRC.
"Fix it 'til it Breaks."

Jacob - EiC & Director of Technology
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