Well that would really suck. I know the storage bins are suppose to be water tight, but my driver side gets water in it sometimes when my friend is splashing the boat a lot with his ski. I keep my phone and wallet in the purple thing and they always do fine.
Thats odd you are getting water under the pull out thing and the cooler.
my cooler has a lot of condensation coming off it and i have gotten lucky its not enough to hurt anything.
I think I would try to rig something up for the ipod. Maybe take a litle rubbermaid type plastic container, cut a hole in it for the cable to pass through. Put the ipod in it and put the lid on, then seal the hole for the cable with silicone. Might look kinda odd, but its where nobody would see it.