As far as I know when it comes to the Diesel vehicles.... The pump in the tank is just a lift pump to help supply fuel to the main injection pump which pressurizes it for the injectors.
The more I am reading, these guys don't actually have a clue... especially if they are charging £760 + VAT for the in - tank fuel pump swap by cutting the hole in the floor... I'd expect that sort of price (well closer to it...) if they had dropped the tank and done it properly.
But that aside for the moment - fuel quantity actuation is done inside the FIP, as your local garage have said... And as it keeps coming back to, but the garage seem to be discounting is that if the seals have been replaced and the pump timing not checked, then that will most likely give this kind of error.
Rather than type it out, I'll copy and paste a few bits from the Electrical Troubleshooting Manual for the Diesel section:
Fuel Temperature Sensor
A thermistor is also located inside the injection
pump. The fuel temperature sensor signal is used to
adjust the quantity of injected fuel, especially during
temperature extremes. The signal is also used to
back up the Engine Coolant Temperature Sensor
(X126). If this sensor fails, the ECM (Z132) uses a
substitute value of 60C and only slight effects on
fuelling may possibly be noted.
Fuel Quantity Feedback Sensor
Located within the injection pump, this sensor sends
the ECM (Z132) information regarding the actual
quantity of fuel injected. Failure of the sensor or
corrupted signals will illuminate the warning lamp
and cause the engine to stall or not start. A second
check, a plausibility check against the needle lift
sensor, also takes place.
Fuel Quantity Actuator
Once again located within the injection pump, this is
a moving magnet actuator, failure of which will cause
the engine to stall or not start as the ECM (Z132) will
activate the Fuel Shut–Off Solenoid (K111).
(Solenoid Valve Injection Timing
This is another actuator within the injection pump.
The ECM (Z132) receives a signal from the needle
lift sensor and attempts to correct the injection timing
accordingly. If a change does not occur, then the
ECM (Z132) assumes a fault exists, activates the
warning lamp and reduces the quantity of injected
Fuel Shut–Off Solenoid (K111)
The Fuel Shut–Off Solenoid (K111) shuts the engine
down if the ECM (Z132) detects a major fault.
Failure of the valve itself does not activate the
warning lamp, although if a short circuit occurs, the
engine will shut down.
So all of that is done in the FIP - and reading that, if the injection timing or the fuel quantity is out, then you will most likely get power problems. OK, the in tank pump may have been faulty aswell, but the issue to me lies in the FIP, and if they haven't checked or adjusted the top of the pump since the seals were done, then as far as I'm concerned, they are wasting their time, your time, and your money chasing around other things.