Ok first I assume you have the water tube installed up in the exhaust housing right. NOT the gearcase, too hard to line up like that.
Put grease on the end of the water tube hanging down, and on the grommet on top of the impeller housing that it slides into. This prevents it from pinching, and binding, causing a restriction in the flow of water.
Put the shifter up into forward gear, to get it up out of the way for now.
Be sure you have a new o ring on top of drive shaft, with fresh grease on splines. NOT on the top of the drive shaft though. Just the splines and o ring.
Push down on shift rod on gearcase, to put it into reverse.
Now slide up the gearcase, until the water line just about is going into the grommet. Ensure it slides up smooth and straight. The grease will help.
If it stops about an inch short of mating, rotate the prop. This will turn the drive shaft, and engage the splines with the crank. When they mesh, it will slide up the rest of the way. Install 1 of the bolts to temporarily hold it.
Now get needle nose, and pull the lower shift rod back up into neutral. While holding it with the pliers, shift motor back down into neutral, and guide lower shift rod into the coupler. Ensure that the detent in the rod, is perfectly lined up with the hole in the coupler, then install bolt. Test the gears, by shifting handle, then turning prop, to ensure neutral is free, and forward/reverse engage. If all is well, install remaining bolts.
All done!