350 Injector Pump

[splam]

I posted about an issue I had this spring with water getting in my 350 diesel motor and having to rebuild it. I put cylinder's and pistons in it, had the head done and put it back together. When I went to start it an old problem with the starter plagued me so I pulled it and had it rebuilt. Everything should be read to go right? Not so lucky! Bleed the fuel lines and have good pressure the injector pump but no fuel when cranking the engine at the injectors. When I pulled the engine I left the injector gear on the pump and pulled the whole front plate on the engine which holds the pump and the water pump so I would not have to mess with timing the injector pump. But I set the whole unit on the floor and the pump shaft pulled out of the pump. When I timed the cam & injector pump I made sure I used the 3/6 cylinder mark on the time gear but I wonder if when I pushed the injector shaft and gear back in I have the rear spline on the shaft 180 degrees off? If I did wouldn't I still have fuel pumping to the injectors but not at the correct times injecting to the cylinders? If that is not the issue does anyone have any ideas what could be causing no fuel? One other thing I did see in the service manual is that I was supposed to wire the control arm WOT so nothing could fall out inside the pump, I did not do that, could that be my issue?

Thanks for the help.