On the mold issue, it looks like a combination of "artillery mold" and some form of fungus that may have been on the wood, not sure. I'm leaning against the on-wood thing, as the sides are book matched strips and the problem only exists on one side. I tried just sanding down the poly and repairing the "bad" spots, but I had penetrated the wood initially, so it came out splotchy. Best way now is to just take it back down to bare wood and build from there. Probably take me a week or so to do.
EDIT: I think I just realized what the other contamination is. I think it is outgassing of the cedar into the poly. It was at the same locations as the artillery spores, so I assumed it was another type of mold. Looking more closely at it with a magnifying glass, I see it is actually bubbles under the poly. I'll still do a full strip down, but will now use my heat gun to heat the cedar prior to applying the poly. I forgot about needing to do that sometimes on soft woods.
On the windows, yes I have thin mesh screens set inside and attached to the wall. I also have door screens I made using magnets to hold close. Have very few biter problems (knock wood).
dave