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John,
Have you checked the voltage while cranking ? Does your system have a voltage compensation map ? If you are cranking up the pulsewidth and the engine is not flooding, low voltage may be an issue. I have a couple of Haltech EFI conversions that will never fire when cranking if battery voltage drops too far, but fire up immediately with a new fully charged battery. Some systems have a minimum voltage to open the injectors and a weak battery, bad connections or a worn starter is all it takes.
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Paul
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