Oil pump hell.

That's a possibility, I believed I was in all the way because the rod was actually a ***** to get out, but i could be wrong! Gonna tap it down gently with hammer handle this time to be sure.
You might lightly snug the pump bolts then drop in the intergear then torque the pump bolts. this'll give a better hex alignment. it is a good plan to in addition install the dist & its clamp to lock in the intergear in case you forget that the intergear can drop out & hit the floor if you flip the eng to tighten the pump bolts. I hate stupid mistakes.