Is your DEF tank still installed and wired in? Might be your DEF pump still pumping. Unplug the big bale connector on the frame near the back of the DEF tank.
Take your bleeder screw loose at the factory fuel filter and turn the key on until you have fuel. Then crank until it starts.
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Oh I'll be interested to install one of those in my truck! This fass POSKennedy pumps are completely silent, if I can make a recommendation. If you get the harness with them, there is an oil pressure switch that turns the pumps on with the engine on, the pumps will prime at key on engine off for a few seconds like a gasser does, then shut off, and there is a button on the controller you mount to the firewall that gives you manual operation for things like priming fuel filters. It's a really slick setup. I have Kennedy twin pumps on both of my trucks.
Have you called fass and talked to them? I've yet to have one that I thought was abnormally noisey.
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http://www.kennedydiesel.com/categoryresults3.cfm?Category=3&SubCategory=157&SubCategory2=125
I have the twin pump deluxe kit on my LML.
Also added a Mega filter setup after my factory fuel filter.