This may be a wild shot, but it's a cheap thing to check, and will at least rule out fuel delivery as the issue. What if the problem is the BOAT, and not the rebuilt engine that had the same issue before the rebuild? How could that be, you ask? What if the fuel tank isn't venting properly - such that by the end of the day the engine can't "suck" enough fuel from the tank? As you burn fuel, the tank collapses due to fuel drawn out, but air is slow to leak back in. This could add up by the end of a day depending on how much you run, etc.
Connect an external tank to your engine when it exhibits the problem and test drive. If the problem suddenly disappears, maybe the issue is the boat's fuel system. I once had a fuel selector valve that had malfunctioned, restricting the flow, and therefore the power.