Can reach in with a small phillips screwdriver to pull up the coupler if the lower rod drops down down while trying to get the thing together.
First thing I like to do is open up the brass coupler just a little to make sure the rod end is going to fit in fully with the bolt through the slot. (would do that while the l.u. is still off.) When you have the rod lined up upon reassembly, use a flashlight and a pick or punch (or small Phillips screwdriver again) to make sure the rod end is inserted fully, or you will not get it to shift correctly and will wonder why. It's possible to pinch the tip of the rod, incorrectly clamping it in place (and increasing the overall rod length) -- might look right, but won't work right.
couple of ways to get that bolt started -- socket with the hand driver to fit in the narrow opening, or one of those small but powerful little magnets on an extendable shaft (bolt is typically steel, but surrounding leg is aluminum.) If using a socket, can magnetize it or the bolt, or use a bit of grease to hold the bolt in the socket, or a piece of electrical tape lightly around the shaft. If you drop the blasted thing, you usually have to pull off the l.u. and tip it over to retrieve the bolt -- hopefully, without losing it on the shop floor. (Same is true for the socket....)
Are you getting the water tube lined up with the grommet OK, and the driveshaft ready to slide up -- along with getting the shift rod lined up? If the driveshaft is a problem, may need to rotate the flywheel a little by hand (always clockwise) -- gears have to mesh. It's usually easier to do the reassembly with the motor in a tilted position.
[edit. Assume you are attaching a couple of the l.u. bolts a couple of turns to hold the l.u. in place while trying to fully reassemble. If so, maybe you have gotten the bolts a little too far in -- can back them off just a little to give you more room to work. When you finally have everything in place, you can usually lift the l.u. with the gearshift handle -- would do that while lifting the unit into place. Should slide together, but don't force it.]