Thank you for the question XXXXXXXXX,
This type of issue is most often caused by a air leak. A minor air leak at that. We need to install a clear line before the fuel lift pump. We are looking for minor air leaks in fittings and connections or possibly o-rings on filters and such.
What is most likely occurring is when the air makes it to the injection pump the engine looses power from fuel starvation but the air bubble is so small that before the engine has a chance to die completely the bubble is driven through the system.
Clogged fuel filters and air filters will not cause the engine to perform in this fashion, because once the engine is starved it generally will stay starving for fuel or air and remain at the reduced power output. Clogged air filters cause smoke, due to the richness of the fuel burn and the unburned fuel in the exhaust.
Short answer; We need to look for a small air leak in the fuel deliver system. Possibly the fuel valve is leaking air from the handle seal.
Marine Mechanic
21 Years Experience as Mechanic, 18 Yrs Boat Yard Owner/Mechanic, Factory Certified