I'm doing this same thing today. I spun the prop while applying light pressure upward, and felt it slide into place. The shift rod slid right into place, and I could clearly see the notch line up with the bolt hole, and tightened it in place. I had removed the pickup tube and slid it into the upper grommet first, and watched it slide into the lower grommet at the pump as I pushed the lower unit into place.
And now I can't get it to go up all the way. I'm afraid to force it, but I'm really not sure what to do at this point.
Edit: Never mind! I set it upright and it moved right into place under its own weight. Anyways, I've used this forum a lot, glad to finally be a member.