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Try this:
1. Remove secondary fuel filter cap (ontop of engine).
2. Cycle the key, leaving it on for 15 seconds each time, do this for 5 times.
3. Check for fuel entering the secondary fuel filter housing, it should fill up.
Sounds like you may have air locked the fuel system, no big deal. When you started the engine and it ran for a few seconds and then cut out, it was running off of whatever small amount of fuel was left in the secondary fuel filter housing, the lines going to the cylinder heads, and the cylinder heads. Do the above and see if the bowl fills up. If it doesn't and the fuel pump is working (should be noticable when the key is on for first 10 seconds of key on) you might have to pull everything back apart and double check everything went together right.
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I'm a mod friendly Ford Diesel Technician located in Sacramento California area.
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