Try installing with the lower unit and remote control in Neutral. You'll have to have an assistant or long arms to turn the flywheel in order to engage crankshaft with driveshaft while installing the L/U.
You can carefully shift the L/U to Neutral by cushioning the shift shaft with a shop rag, then grabbing with Vise Grips or other suitable pliers. Rotate CCW until you find Neutral.
If you find that you have trouble getting the shift shaft and upper shift rod aligned when installing the L/U, you may have to undo the shift cable from the shifting arm and slightly reposition the arm. Sometimes the shift cable is "preloaded" and causes a slight misalignment of the upper shift rod.
Hope that helps, let us know what happens........ed