Have you considered mounting the core on the (non-mobo) side, and ducting air through one or two drive bays? It would give you a fresh intake at the front, and an outlet at the back. You can then ventilate the rest of the case any way you see fit.
I'll be using a blower in my Chieftec server case, and I'm opting to setup an intake on the side (with filter), and outlet the back, where the core (~6 by 8) will be. Anything else will have a set of small quiet fans, for positive pressure.
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