My 2000 boat was like that, too. Not really a lip, but sort of an indent above the bottom edge. Probably had something to do with the reinforcement at the bottom of the well.
Karl, what about one of those hook shaped knives that the ferriers use? It's sharp on the inside of the hook and you could use that to scrape off some of the epoxy and then get it smooth with a rasp or something?
How far up does the carpet go? Just along that lower band, or all the way up the inside of the daggarwell?