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MSK-1

You are on the right track. My boat also has the pump discharge and wires going to the tank compartment but mine fit loosely inside the pipe. This is where the water will drain out of the tank compartment. This is the only drain you have so you have to get it where water will flow through it. This may be your problem. I have never pulled my deck plate. It looks simple enough but I would count on it being stuck from caulking and dirt and grime from years of use. If I were you that is what I would do next. The problem will reveal itself when you get the deck plate up.
Good Luck
Carter