JD 850 3 CYL DIESEL INJECTION PUMP PROBLEM

I have a John Deere 850 tractor. It's a 3 Cylinder Diesel with Fuel Injection. I ran out of gas, and I noticed the fuel line was leaking (tank to filter) so I replaced all the rubber lines and filled the tank. Now it wont start. I removed the 3 hard lines from the injectors on the top of the engine and I'm not getting any fuel. I removed the hard lines that exit the pump and no fuel there either. I removed the INPUT rubber line from the pump and hooked it up to a jar of gas (bypassing the filter and tank) and I am getting no suction. So I removed the fuel pump. It's a square pump made by YANMAR and it has three "lifter" looking things that ride on the camshaft of the motor. They are each connected to a piston looking thing that pumps the fuel out. The pump has a strange flat lever with teeth that contacts each of the pistons of the fuel pump. I think it has to do with timing the pump. Upon removal of the pump, I lost the timing settings. The teeth disengages and its all out of wack now.
I made some phone calls and someone suggested that I probably just had some air trapped in there and that would keep the pump from working!! They suggested I should put everything back together and try pressurizing the gas tank. But now I cant get my pump back together correctly! What should I do??? THANKS

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