Guys, I'd like apologize to you as this was all a false alarm. After I removed the oil pan, it was plain to see that the rods were indeed installed correctly!
It was just too hard to see the squirt holes though the top of the engine. After I looked again, I could just barely see them. Turning the crank might have helped position the rods a little better too. They just weren't very apparent before.
Now I know why I didn't have any indication of problems when I was assembling the bottom end.
