Get some large diameter electrical heat shrink wrap (I've seen up to 3in) peel back the tops of your hoods, add wrap and heat until snug - voila! You could also pre cut a hole for the shifter paddle and cover both the front and back openings (not sure if that would affect the shifting, but it's worth a try).
I guess you cut off and replace whenever you replace the cables?
I dumped my shifter in the sand at a USGP last year and was able to flush it out with White Lightning Clean Streak degreaser. It's worked 100% since.
by "flush it out," how much are we talking? while on the bike, soaked it, sprayed it in forcefully?
(forgive the newbedness)