Well I found the source of the smell....it is this sealant or epoxy the put on to..well seal the seams I guess..
I imagine this smell goes away after awhile?
Ideas on the crooked flue? Am I over analyzing? Am I expecting too much? This guys seemed like a very knowledgeable plumber and didn't say anything about it...didn't even mention it.. when I saw some condensation the first time we fire it up he said yep, watch your hand because it gets hot under there....