04' Cobra metal top leaks

How does the water sealing system on a Cobra normally work?

On the inside lower edge of each side there is a small trough. (A great place to store the TE probe, etc.)

If I look closely, there are small high water marks in there. Also drain holes at the front and rear ends. (One of which was clogged.) From experiments with a hose outside, it looks like a little water is getting by the rubber trim piece/rub rail on the outside. Looks like a possible design was if water goes out faster than it goes in, all is well.

Except there was a bit of carpet dipping down in the trough which wicked water up and over the side to the glider. So I'm wondering if anybody here has looked at how the seal system around the lower sides of the trailer top are supposed to be.

I may have to rethink where the nice shiny TE probe is stored as well.