Add a little lube to the connector to make things easier. Remove the top bolt, and pry the connector apart at the top just slightly with a bladed screwdriver. Look at the end of the upper shift rod. It has a machined indentation to allow the bolt you removed to slide through. The rod has to be fully inserted for the indentation to be in place.
Assemble the lower unit first, short of connecting to the upper leg. You have a long model. Best to have the motor attached to the boat transom or to a stand. Place the gearshift in forward or reverse -- whichever extends the upper shift shaft. Lift up on the lower shaft to get extra height (may have to rotate the prop).
Now the tricky part, at least the first time. Lift the lower unit into position fitting the driveshaft into the powerhead, and the copper water pipe neatly into the rubber grommet at the impeller housing. At the same time(!) line up the upper shaft with the connector and slide the shaft into the connector. There should be just enough room to reinsert the bolt as described earlier. Tighten the bolt and carefully raise the lower unit into place. Screw in the bolts and torque them evenly, and you are done. The shift rod length is not an issue. If fitted properly into the connector, all gears will work properly (don't force).