If you go with McMaster-Carr check the differant noise foams for the sound reduction rattings. The 1" with surface film and adhesive backing there carrys .8 rate. The egg shell foam they have 1" thick isn't as low a rate, but a good second layer if your water loop case is large enough. The McMaster's stuff is good & lower cost than the B-Quiet foams. Up to you to decide how much you are willing to spend for the amount of noise reduction you need/want & how much space you have for the foam to fit in.
If you plan the water loop case large enough you can also mount the PC case on top of it. Then just cut two holes in the top of your water loop case, and two in floor of PC case for water lines to run through. This allows the smallest floor area requirement for whole set up, although does of course make things taller. But the water case under the PC case does a couple other things as well, 1) keeps lines short & straight as possible. 2) If any leak were to ever develop in the water case it can't damage any puter parts.
The answer to the pumps heat is this. Place rad also in pump case close coupled to the pump & two, or more, rad fans. These all go near to center of the pump case. Baffles as your father said contain the noise. Air comes in one end flowing around baffles & out the other end, still flowing around 2 or more baffles again. My design is a wide box that allows setting my MD20Z Iwaki in sideways to reduce the length of box needed. Turn pump outlet to the side & low insead of up, directed into rad inlet which is on it's side to lower overall height needed. Rad outlet is now on top & the end with the inlet/outlet is 1/4" higher than other end to aid in air evacuation from inside rad. The rad fans are mounted not on the rad but in a 1/8" mahogoney panel that fills the inside of case top to bottom & side/side pulling air through rad and flowing around pump. Both the rad/CPU/GPU heat & pump heat go out together. Pump is sandwiched in between the rad in it's panel & the panel with the fans. Fans are in panel high enough to allow better air flow over top of pump.
Reading the above, I'm not sure I'd understand it well enough so let me try again.
From front to rear.
1/8" mahogony underlayment panel with cut outs for air inlet & filter => gap => baffle (all baffles are foam covered) which takes up a bit over 50% of opening => gap => second baffle come'n from opposite side or top/bottom also covers a bit over 50% of open area, and so overlaps with first baffle => gap => Full size panel with rad mounted into it => as close as possible to rad the pump which is close connected to the rad inlet => full size panel with dual fans pulling air => gap=>baffle=>gap=>baffle=> OUT evil heat! ! Trapped evil noise! !
Box is 15" wide X 11.5" tall & 26" deep for a Lain Li PC 76 server case which is wider & deeper than standard. Box still is 2"+ wider on all sides/ends than the server case, add some home wood trim that doubles as a added insurance of case not moving & looking good. Yeah, huge case, but you can adjust as required for your use.
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