You're not going to like to hear this.... but if you had the head off the pump and the delivery valves removed from the head... you need to have the pump spill timed. The issue being that number one needs to be timed to a reference and 2/3 need to be degreed off of #1. This way you know with confidence when you install the pump to the flywheel timing marks that the time is right so to speak.
Second issue... your injectors, for whatever reason... are not firing.
This is probably one of those times where you're best off to pack the whole works in a box and send it off to an injection shop. Be up front with them about what you've doen so they take the time to go through it and get it right... and just have them install new nozzles in the injector bodies.
When you get it all back make sure you install the pump on the correct stroke on the engine if you're not already positive that it isn't 360 degrees off...
Again, I say this... I know you probably don't want to drop that kind of money on having the pump spill timed... but IT WILL BE CHEAPER THAN A MELTDOWN or cracked piston if you do succeed in getting her running with improper timing.