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well... i was thinking about putting a very small hole, like a pencil sized hole... kind of like the one i use to put water back in to the dishes... i think that's how LG's work... right...? the fan goes right over one of the vent holes to pull fresh air in... that's probably what they mean by forced air incubators... forces small amount of fresh air in the incubator via fan... 
i don't think so... as long as you have the air going thru the heating element, you'll be fine... i use a temp controller, and i don't stress about that really... i know eventually, the heat will go up and the controller will turn off the bulbs... and vice versa...
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i know my holes are too big, so maybe your holes are too big too... you don't need that many holes for ventilation... how many eggs are three trays...? 90 eggs...? you could've just put  a small hole near the fan to pull in fresh air, and leave one hole on the side or so... that's more than enough ventilation if the fan is pulling fresh air... that's how i'm going to build my next one... 
anyways... i'm thinking you have too many holes... plug some up somehow...
yeah, that's a lot of holes man... mine only has two holes... you have like, five holes right...? some people only rely on the air that goes in thru the holes for the cables... i sealed those off because i like to think i have more control over everything...
good luck...