As someone that's spent some time in the cockpit at FL410, I don't think the wooziness is related to the air circulation at all. The air always seems fine up there. No mid-flight sleepiness. Keep in mind that what you experienced could be related to a lot of different things, including fatigue, boredom, dehydration (I drink sooooo much water on planes because of this). I'd suggest getting a good book, drinking a lot of water, and taking a nap if you feel tired.