Actually.... there are 3 pumps on the 240 EFI engine.
1) High pressure pump. This feeds the injectors, and is in the vapor tank.
2) A pulse pump. This is the low pressure pump that feeds the vapor tank WHILE THE ENGINE IS RUNNING.
3) An electric lift pump. This pump pushes fuel though the pulse pump, and feeds the vapor tank while cranking only. Basically, it's an electric version of the pulse pump. At cranking speed, the pulse pump can't deliver enough fuel on it's own. But once the engine is started... the pulse pump pushes plenty of fuel.
Since there is a redundant pump in the system... both the lift pump, and the pulse pump not only have to do their job at the right time... but they also need to be free flowing when NOT in operation. This is something that gets overlooked. SO.... assuming you can draw fuel up the feed hose before the lift pump... you should also be able to draw fuel up the hose before the spin-on filter. (after both pumps) If either is dirty internally... then there can be issues.
Brian has a good point. In more than one occurrence, I've seen the needle and seat in the vapor tank be corroded, and stop functioning. But, if fuel isn't flowing in.... it can be observed with either opening the drain on the vapor tank, or putting a pressure gauge on the high pressure regulator.
Yes... the 200 opti, 210 carb, 240 efi (gen 1 & 2) all are based off the 2.5 L Merc powerhead... and they all run similar. BUT... they are all a little different. Regardless... there should be no guessing. I thought you took it to a real shop... but it's perfectly fine to have a buddy help out.
But, before I give anymore help.... I want to know the exact compression on each cyl. Over the years... I've tried to help people, and it turns out to be a roasted engine. Even a bad set of reeds or a broken hose on the bleed system will show up as low compression. This is not a test to looked at lightly.
Also... I want:
1) Verification of fuel flow. (mechanical)
2) Verification of pump function. (all 3)
3) Verification of fuel pressure on the high pressure rail.
The high pressure pump shouldn't come on, until the key is in the "on" position. But this is easy to verify. Just put a meter on it, and watch the voltage. As I recall... the ECU controls the ground. SO... the hot wire is ALLWAYS hot. That means... if the other wire has gotten shorted to ground... the pump will run. SO... check the ground for a short to ground. If you find it shorted... pull the plug on the ECU, and check it there. It should be "Open" until the key is turned on.