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Agree with E, you probably put a large air bubble in your fuel lines when you drained the separator. Bleed this out and you should be good to go. However, with 2-3 cups of raw water in your system you will need to play close attention to your water separator until it is all worked out, meaning lots of draining and bleeding until the water is gone.
Imperative that you do not allow water to reach your injector pump!
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