dynamat, roofing membrane, etc. will help (a little) with stopping the transmission of sound by helping make the box acoustically dead. to stop the sound you'll need to seal it in the box. No holes. sourounded by closed cell foam. now you get major heat issues since you've made a small insulated box. Especially with MDF. It does not transfer heat well at all. Though it may work with thick metal. Heat pipe?
try a different apprach?
figure out what the noise is. If it's the water going through the lines, that sound is just (more than likely) going to transfer through the lines.
If it's the pump itself, try isolating it from the case. rubber or closed cell foam pads. Using points instead of a base, less surface area to transfer vibration.
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