Post may be a bit late for your needs, but anyway......
(Goes without saying, but if you have the PSU case open / tampering with it - make sure its unplugged and allow internal capacitors to discharge for a while - otherwise you might get hell of a 'belt' from it - not funny!)
Part of the noise problem with MDDs is that the PSU case 'clips' to the internal side panel on studs thus transferring any noise and vibration directly to the panel - much like a sound board.
Its difficult to put much in the way of packing between the two without making it impossible to re-locate / refit the PSU on the panel, but I've had some success with thin strips of Chamois leather.
There are two in the leading edge ( just above optical drive )....these can get very noisy as the bearings start to get loose over time - all the noise is amplified thru' the side panel (see above).
Often its only one fan causing the problem - you can test which by carefully and quickly stalling each of the fans using a small plastic stick or end of a modelling paintbrush gently pushed through the grating.....DON"T push metal screwdrivers in there - its a PSU !
Be QUICK about doing this - you've got the side panel open so you don't want to leave your CPUs 'cooking' for very long!
iF you determine that one or both fans are noisy (rattle), then you need to replace them.
In my experience, don't mess about trying to improve / repair the existing ones.
The units are fairly stock 50mm items and only use a ground and supply wire (red and black). Some replacement fans also have a speed feedback wire (often yellow) which you won't need / use.
Be careful about mounting the fans squarely in their rubber seats and you will probably need to splice the board connector(s) from the old fan(s) unless your replacements have similar connectors (unlikely). This IS a time to use solder and heatshrink - twisting bare ends together is not acceptable in a CPU case....or in any case to be honest!
Re-assemble and test.... making sure that they DO actually run AND that BOTH fans turn on / speed up when things get warm.
Will they be 'silent' ?........No.
The OTHER source of fan noise is the main 5" fan that primarily cools the CPU when the door is shut. After some years of service the bearing gets rattly and somewhat irritating - again you can check by quickly stalling it (as above) to see if the noise goes away.
The fan slots into a carrier under the optical drive(s) and is generally not that hard to find a replacement for.
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