Could there be a problem still with mold or mildew from the water leaks that you've had, Corin?
You may very well be having some kind of allergic reaction to mold that is residing somewhere?
Forgive me if this ground has already been covered.
I think the mold itself is gone. He removed all the bad wood. But it's likely still that the stirring up, along with the fact that we're still moving furniture and crap around is irritating all of this.