One to add to Dens list, fuel tank breather obstructed, i.e. is the fuel cap vented properly?
It could be that air is not getting into the tank causing a ‘vacuum’ restricting the pumps ability to move fuel through to the carb if as you say, the inline filter is empty, or:
The fuel feed line from tank to pump is collapsing internally, possibly due to the effects of ethanol in modern fuel.
You can now get fuel hose that is ethanol resistant to 10% (current UK limit) or 15% and I’m in the process of replacing the fuel lines on my TA and DS as a precaution as the hose I replaced less than a year ago on both cars is already showing signs of ‘softening’ and ‘swelling’