Why did you choose that orientation for the MB? Just from looking at your pics, it seems like if it was on the other side of that wood piece so the slot side of the MB was facing the rads, it would get a lot more cooling air. Wont most if not all of the blower air be exiting through the rads? If so there will be more airflow on that side than the side of the case the MB slots are facing now.
Also think about how you are going to do the filter now before you continue, so you can build ease of cleaning and (even better!) a large surface area filter into the design if you can. One of the filters on my PC is on the bottom and its a bitch to clean. Plus its small which means it needs attention on a monthly basis. I regret that now. Maybe you could design a small airbox under the blower with a disposable house filter that slides in at the bottom. That size filter could go for 3-4 months without being cleaned or replaced.
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