Well, I dunno... but it sounds like you need to back the fawk up and start over from the beginning.
From what I'm reading, you've got a no-start with an unknown-condition injection pump with fawked up seals and an improperly-sized woodruff key. You're not sure the pump is timed correctly. You think it's bled, but elsewhere Ken was talking about starting it on a single Optima yellow top. IME, the likelihood of getting the fuel system bled on a single battery is between slim and none.
When we replaced the pump in the 6.2, it took two brand-new 1100CA batteries with generous recharging times from a wall charger *plus* a jump from a running vehicle just to have enough battery to crank it until the injector lines were cleared. That truck fires immediately under normal circumstances, but it had to sit there for a damn long time and sputter before it lit the first time.
I will say this.. Everytime we took the front apart or the pump off we made sure that everything was lined up like it was the very 1st time.. and YES I am sure we have it at TDC(top dead center) so NO we did no take the engine apart incorrectly...
And like John said yes we have gone threw a few batteries and yes we have to charge the batteries every night.. I even bought a new 1000CCA battery to use as the primary..
But for now the Truck is at my house thanks to Richard( last nigt) so it will sit and stay until I get back in 3 weeks..