This is what I've been trying, minus the pliers. I have not been trying to put the pump on, BUT JUST THE DRIVE SPINDLE FOR IT, I may have not been clear enough when I stated it before, but thats what I've been trying to do, just get the spindle in place, then I can line up the pump and dizzy.
I checked the spindle again, and it still appears to be straight and true. But for some reason when I push the spindle through the lower hole, and trie to get it to come up through the upper hole(dizzy hole) its slighly off, maybe a 1/16-1/32 off, so it can't be pushed up through the hole. I was thinking my timing cover could be seated unproperly, but even if it was, both holes are on the same casting, so adjusting one wouldn't through the other one off, would it?