This is a tough one. You have a new fuel pump, fuel filter, and the feed, and return fuel lines are not clogged. My next question to you is, will the same problem happen if the fuel tank is full? If not, its possible your pickup tube in the tank may be the problem. Other than that, it would have to be the mechanical pump. If it's a cheap one, it's likely the diaphragm inside has failed. Why it happens at certain times, and not others though, I cannot answer. This is a very basic fuel system, so we need to be very basic with diagnosis. I hope this helps. Keep us posted.
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Thursday, November 28th, 2013 AT 5:13 PM