mine leaks pretty bad but I never took the time to figure out exactly how its getting in....pretty common problem from what I have read but I also remember some saying there's don't leak at all....definately check the through bolts that hold the teak runners on....mine are leaking for sure which I need to seal asap....
I'd ditch the carpet first of all .......It's kind of a pain too but I pull my cushions out and put them in the garage if the boats going to be sitting for more than a few days.