Re: johnson 9.9 outboard
First off I like to tip the motor up & lock it into the raised position, easier to see & align than hanging upright on a transom or stand.
Lubricate the water pump tube that enters into the water pump grommet.
The lower shifting rod needs to be turned all the way into the threaded linkage in the gearbox. If it does not rotate enough to align the upper bend to the connector, then unscrew it from bottomed out until it is aligned.
I like to attach the connector sleeve to the lower shift rod first.
Then pull the lower shifting rod UP (into reverse for the gearbox) it is easier to see & align the upper shift rod into the connector as you then try to align when pushing the lower unit up. You can move the shift lever into forward, (lowering the upper rod into the connector). If the lower rod moves down, place a screwdriver under the connector holding it up.
Good luck