Since your setup is so unusual, to test the tank, second pump and filters, I would get a soda bottle, fill it with fuel, and plumb it to the OE primary filter with the return line also going into the bottle. Put the bottle in the cab above the engine and run it this way and see if it runs ok. If it does, the problem lies somewhere back towards the tank. If the problem persists, it lies somewhere on the engine side of the system.

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1977 300d 70k--sold 08
1985 300TD 185k+
1984 307d 126k--sold 8/03
1985 409d 65k--sold 06
1984 300SD 315k--daughter's car
1979 300SD 122k--sold 2/11
1999 Fuso FG Expedition Camper
1993 GMC Sierra 6.5 TD 4x4
1982 Bluebird Wanderlodge CAT 3208--Sold 2/13