The more I think about this, I'm wondering if there was something faulty about the ujoint that didn't allow those 2 caps to get grease. Nothing else shows signs of binding and I would think binding would have caused damage to more than just caps. Especially with the flat spots on the trunion, that's like what happens when the needles aren't getting rotated.
I tried to find the old joint in the dumpster, but I didn't have any luck. I was thinking I could put grease in it and see if it comes out all 4 ends.