Lift Pump or IP timing, those would be my guess. Testing the lift pump is easy - when you had the two fuel lines going to a temporary fuel tank, what was the discharge like from the return line? If that was weak or non-existent, then that is a problem.

IP timing: It is possible to get the IP installed 180 degrees out of time, and the engine will run but very poorly and like you describe. You would need to remove the IP and set the engine to TDC on #1 on the compression stroke, set the IP correctly, and install. I'm pretty sure that your IP splined drive shaft has a missing spline that should be lined up with a mark on the pump body, and that sets the rough timing when you install the pump.

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Respectfully,
/s/
M. Dillon
'87 124.193 (300TD) "White Whale", ~392k miles, 3.5l IP fitted
'95 124.131 (E300) "Sapphire", 380k miles
'73 Balboa 20 "Sanctification"
Charleston SC