Hey Grigg,
How come it is so different top to bottom? Any sagging going on with the mounting, cab or sleeper? Personally (I seem to do things the hard way) I'd probably be tortured enough to get the metal to line up (mounts or welding or re-angle of the crawlthru) then use some simple sealer. To try to close a variable gap seems like it will be less than perfect...my humble 2Cents.