Okay. Sounds like you are losing prime. You have what is called a lift pump that supplies the fuel to the injection pump which turns it to high pressure. If the high pressure pump does not have any fuel delivered to it then it has nothing to pump. Once you give it fuel with spraying it, the air lock is overcome and it starts the engine by pulling the fuel. We know the high pressure side is working because it runs just fine.
I would check the TSB that I provided previously and then if you find no air leaks, then I would put a fuel pressure gauge on the fuel delivery line in front of the high pressure pump. Then just turn the key on but don't crank the engine. You should have between 5-10 PSI with just going to key on. If not, the lift pump is probably your issue.
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