Eric,
I’ve been giving your post some more thought and examining the rain baffles and now I think I get it. As you said, the weather stripping is a bad idea. What was happening is that it was holding the water in so that instead of flowing out the bottom of the baffle it was forced up and into the cabin. The only problem is that if I re-install the baffles there still will be no way to get an air seal when the covers are closed–I think because of the way the flanges are mounted on the inside.
So I’m going to try it the way I have it for now. If I’m still getting water in I’ll remove the weather stripping and replace the baffles. I think I can find all the “plugs” I drilled out of the liner. I can use them to devise covers for the vent holes in cold weather.