Does he have receipts for the engine replacement? If not who knows for sure what was installed? Providing the engine is the correct block with the correct heads, and the correct ignition system. It's likely something relatively simple, like fuel supply (carb), timing, or weak spark. Carb's can be troublesome especially if you have a vacuum leak at the base of the carb (most likely spot on a boat). If he's installed an automotive distributor rather than original equipment your timing will be all messed up since cars generally use vacuum advance, boats do not. faulty spark plugs or a weak ignition, can cause most of the issues you mention in your post. Because your problem seems to worsen at 3000rpm it seems to point towards a weak or failing ignition. Check the ignition components are the correct ones, check timing both at idle and insure it's advancing as it should, by 2500 RPM you should see roughly 28 degees of advance give or take. If that all passes then install new spark plugs. If no change your likely looking at a fuel issue.