Myron,
I know that I am not a trucker, but if it were my setup, I would try to avoid mounting the tool boxes any lower than the frame. If you want extensions further down, use some flexible plastic or rubber. As for a gap filler, chase the huge one between the trailer and truck (lower portion behind super singles and above wheels below trailer).
http://wattsupwiththat.files.wordpre...ck-savings.png
Just some ideas.