Check the fuel pressure, should be around 40 PSI when you turn the key on if memory serves. Check it under load too, it should stay around 40 PSI. If it's low, the fuel pump could be the problem, the fuel supply line could be kinked, or the filter might be clogged (not likely with a brand new filter...)
If the pressure is good:
Swap the MAP (manifold air pressure) sensors from one engine to the other and see if the problem follows the MAP. Do the same with the CTS sensors (coolant temperature sender). Perhaps one of these sensors is failed and making the engine lean out. Does not take much of a lean mixture to cause what you are describing when on plane. I doubt it's the crank position sensor, but you could try swapping those too.
Does you hear the classic Merc double beep (it's the boat equivalent of a check engine light)? If so, the ECM (should be a MEFI 3 or MEFI 2) will have code(s) stored and they can be read by a scan tool.
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