All you really have to do is toss the snorkel and cut out about half of the top of the airbox lid. I cut out the entire recessed section towards the rear of the bike, about 3"x5". This is the recessed section that holds the snorkel.
Make sure the little rubber-sealed drain hole at the bottom of the airbox is free from dirt/mud/etc, so that if any water does get in, it can drain.
This allows you to keep the CDI box in the same location, and offers at least some protection from water.
The search capability on this site very useful for finding out details like this. I posted this same information before, so you'll probably find it. Give it a try, and good luck!