If I correctly understood what you wrote, it sounds like the layout is the same/similar to my Ariel. Is it possible that you have an Ariel hull? On the floor underneath the two steps leading up to the cockpit there is an opening, about 8"X8" I would guess (It is covered up when the steps are in place). When that lid is removed, you look right down to the deepest part of the bilge - which is where my electric bilge pump rests (and the inlet for the Whale as well). It is narrow enough there so that the pump can not tip over (the electric pump I mounted on a board per instructions). The second cover you referenced is where I store beer, and that takes priority. Beer I use frequently, the pump only once in a while.

My boat sank in the Chicago Ship and Sanitary Canal, and cleaning the bilge was the last major task. I didn't know what I would find. Ebola? I used a good strong detergent, washed it several times, and coated it with Gluvit, an epoxy that remains flexible and can take pressure from the contact side (like water trying to get in). Then took several Turkish baths.

It sounded like your fourth cover was in the motor well. Right? Wrong? (Is your boat an inboard or an outboard?) Is there any chance that the black stuff is oil from an engine that has collected over the years?

What I don't understand about that fourth cover is that if it is forward of the motor lazarette, any water would run right into the deepest part of the bilge, immediately. I clean out the boat by srpraying water under the cockpit floor and let the water drain right into the bilge, start the pump, and the whole thing is done faster than I can get out of the wet clothes.

The only place junk wouldn't drain immediately would be from the stern lazarette, which is supposed to be sealed from the main hull. It is conceivable that that lazarette has bad stuff in it and is slowly leaking into the main bilge through a leak. Is this a possiblity?

Or is this really a Commander and I'm talking about a different layout?