I don't know much about the 3.0d but I know that on my freightliner I had a a leaky fuel line on the low pressure side of things and even though it didn't noticeably leak that much after I changed the fuel line it starts much quicker. My assumption is that the line was leaking and getting air bubbles when it sat and then it had to take a couple seconds to pump through. If you have low pressure in the rail I wouldn't think it could be an injector.

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2004 e53 m54 with 6spd manual