The seal doesn't do much to be honest, the water gets past and drains down the drain hole. Sort of what happened to me. Except the drainhole wasn't attached and the water went straight into the car.

At work I got an airline and blew air straight in and lots of muck came out the wheel arch. Alternatively if you don't have access to compressed air, get a softish length of coat hanger, welding rod, etc and you can push it down the front holes. As for the back, they are hard to get to, to clean out thoroughly so i resorted to parking my car downhill all the time!
My head liner came unstuck over summer, i tried everything to re-stick it and nothing worked, even superstrong sprays, resins etc. You will probably have to get a new one.