Did anyone look into the Innovatech HDD block?
The whole side versus top has been debated here quite often. The bottom line is that the top temp you can expect from an HDD is ~45 deg C, and the only viable solution to cool it is more than likely through the sides, even though it may not be the most efficient. Top cooling usually has to go through an insulating layer, so it just doesn't work. Then there are individual components on the PCB... (results may vary: check your HDD)
(see link in my sig) So I opted to make side blocks, and provide room for air cooling those small components, with heatsinks added. The blocks can run in parallel within my loop, for minimal impact, and still have enough flow to actually do something. A 40 mm fan ought to do the trick, but I've got room for an 80 mm.
Rubber grommets or mounts ought to keep the vibrations from reverberating through the case, if not, I'd just hang/suspend sound baffling plates. For the level of cooling it provides, there's no sense in an extravagant solution, IMO.
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