Thank you for the updated specs:
Just three immediate thoughts as custom cooling requirements are going a bit out of my comfort zone.
1) PSU: make, model, wattage, age, condition (original, new, refurbished, used?) Reason for asking: your build needs power and PSU's, of course, generate heat that must be removed. PSU's have their own fans and and the overall placement of case fans could prove counterproductive.
2) For the most part I understand that case air flows should follow natural convection; i.e., warmer air rises so case air flows should be from bottom to top with the top exhaust fans being a bit higher in capacity. As I understand the described case air flows they are to be horizontal from one side in and then out on the opposite side - correct?
3) This: "The reason I went for such design is that I could hide my build under my desk for asthetic reasons."
Understood and fair enough. However, many electronic devices have cooling systems etc. that, to be effective, require some amount of surrounding clearances. Top, front, back, sides. Even with a working fan/cooling system hiding the build may make all cooling efforts moot if the surrounding clearances are insufficient. Both by heating the surrounding space and by bottlenecking air flows.
And the planned case,/enclosure is only 2" (50 mm). That makes it all pretty tight.....
No disagreement with your thoughts, plans, and requirements per se. Just perhaps, reconsider your aesthetic requirements.
Parts cost too much these days and heat is a component killer.
Do not let form get in the way of function.
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Hopefully there will be additional thoughts and comments. If not, moving your thread to "Cases" may prove helpful.
Consider posting a photograph or two here as well via imgur (
www.imgur.com)