Hi Evan
A frustrating problem
But to answer your question
Is it possible the air is entering from the crank case on either the mechanical lift pump or the high pressure pump?
It would not seem so.
The parts list doesn't show a replaceable diaphragm , but the rubber diaphragm would be the only thing in the pump that would give out
The result of a leak in the crankcase side of the mechanical lift pump (fuel feed pump in the parts list) would be fuel in the crankcase as well as air leaking into the line. Do you have noticeable fuel in the crankcase? I have no idea how you would determine this, Smell?
j30.us/files/Yanmar-2GM20-Parts-List.pdf (page 37)
The fuel pump (page 36) has some seals (parts 6 and 13) which would allow a leak back into the crank case but as with the fuel pump such a leak would result in fuel in the crank case as well as air in the line.
So sit down with a pencil and paper and draw a schematic of your complete fuel system.
Note every joint and connection.
Go back to the boat and with the drawing, check everything again,
As you said
Air is entering the fuel system, It will turn out to be simple ,(I hope)
All the best
gary