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It' a 2003. Yes it starts and shut off about 3 time before it stays running first time you start it for the day. (once in a while it will start normal) After you start it the first time it will run and start the rest of the day. I put a new stock fuel pump on and no difference.
You may have a small air leak in the HFCM system. I would check that first - maybe make sure that the HFCM cap o-ring is not leaking for some reason.
The later year models modified the tubing from the HFCM to the secondary filter to include an "anti-siphon" loop. I suppose it was done to prevent what you are experiencing.
The small black "stand pipe" that holds the filter might need replaced or the FP regulator spring/plunger might be leaking. I don't have a detailed flow schematic of the secondary fuel filter housing so I'm not sure that either would apply, but that's the only two places I know that fuel might go back to. Does this happen with a full fuel tank also?
Wonder if the sealing surface of the fuel regulator poppet valve could be damaged? Also keep an eye on your oil level to make sure the fuel is not going that way.
Read somewhere about a bubble test at the secondary fuel housing for another problem wonder if you are getting pressurized from that forcing the fuel out.
Seems like it must have been a common enough problem for them to re-engineer the fuel filter bowl and line.
Note that it is NOT backward compatible for older year model trucks.
My suggestion would be to let the fuel pump "cycle" once or twice upon first start of the day, just like you were changing filters OR add a check valve inline to prevent siphoning.