You could take some perforated rubber shelf liner and put it on the bottom of the top hatching tray except for the portion below where the warm air enters. That would keep most of the feces from falling through and still not restrict air flow. Plus that tray is in the middle so temp should stay pretty constant.
I built one very similar but it is in a large cabinet that has the incubator sitting in the middle of it. The cabinet is huge and the incubator box slides into the cabinet with an air space top, bottom and both sides. The bottom space has a door the hatch tray slides into. There is a bank of fans on the left side just above the hatch space. Above that is the primary heat element. Then over the top of the incubator where the water reservoir is. Then down the right side across a secondary heat element, down to another water reservoir and then across the eggs.
The two heat elements have separate redundant controls. Both water trays are filled from above the cabinet. One is fed by a gallon glass jug working on vacuum.