Re-route your air pick up tube to somewhere that stays dry for the most part. From there put a thin bead od gasket maker around the base of the air cleaner where it meets the carb and then get some decent but thin weather stripping for the top part of the cleaner that you take off more often and seal that. Also on the wingnuts you will have to put a rubber gasket under there to keep the water out. From there just look for any other spot the water can get in and seal it up like around you oil breather tube.
You can make that thing almost like having a snorkel if you take your time to clean everything and search for leaks. Also where you put that pick up tube will be most important. While you are at it take your distributer cap off and put a thin bead around that as well to keep it good and dry. and use a bunch of the plug wire grease on each one to keep them dry as well.
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