WHOSE FAULT IS IT? If you skimp on care and maintenance, you deserve to be left out in the cold. But improper clearances, splashing bilge water, and shafts that abrade intake hoses are the fault of the boat manufacturer that installed the engines. Ask the motor company to deploy a field engineer to "sign off" on your new boat's installation before you buy. If it won't, threaten to select another engine brand, or boat, if necessary.
THEY CHECKED ALREADY. Uh-huh. Except for large yachts, engine manufacturers don't sign off on every individual boat's motor installation. They spot-check a model line, examining maybe 1 out of every 20 engines. Demand that your specific boat be checked and ask that the report include both the hull ID numbers and engine serial numbers. If there's a problem later, show that report.
GASP! Engines, diesels in particular, require a minimum amount of air, measured in CFM (cubic feet per minute), to perform well and live long, healthy lives. Obtain the CFM spec from the manufacturer and place a vacuum gauge (available at auto parts stores) in the engine compartment during your demo ride. If you record negative pressure (a vacuum), you may have problems later.
CALL IN THE CALVARY. Bring in third-party professionals. Mechanics, surveyors, and naval architects can often spot an installation glitch, such as poor water flow or improper geometry, that could cause problems down the road. Their fees are well worth it as a hedge against hiring a lawyer during a warranty dispute.