Switch on the ventilation in the bonnet using the magnet. I think the goal would be to keep it as dust free as possible and protect the pins. If you have a cover and fan, remove or replace the cover. Attempting to use the fan cover will only make the device hotter. Overall the case looks good and the fan could be more comfortable with a better cover. It would also be nice if you could mount it, but I think a few Velcro fasteners on the underside and on the wooden shelf would be ok. I think I will return to the Flirc body in my next project. They just weren't available back then, so I gave this one a try. That's fine, but don't bother with the fan assembly unless you're planning on remodeling the lid or you have an urgent need to cool the pi4.
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