Sorry -- sounds like it might have to come apart again. Have to make sure each of the screws/bolts runs through the machined openings in the end of the upper and lower shafts. If not, the overall length will be affected (close tolerance), and the motor will not shift properly. It's a good idea to open up the brass connector slightly with a bladed screwdriver, just to make sure the rod can slip in freely. (Problem is the connector will clam onto the rod end(s) and fool you into thinking it's hooked up properly)
But, I'll assume the bottom screw in your link is attached properly. See if you can ease the gearcase or g.c.extension bolts out a bit further to give you more room. Put the gearshift lever in whatever position moves the upper rod down (likely reverse). Reach in with a bladed screwdriver and try to lift the lower rod up a bit by hooking the connector. Adjust the upper rod height with the shift lever until just above the connector, then slip the rod down in the opening (may need to use a needle nose pliers to help with the line up). Hopefully, you've managed to leave enough room to install the screw/bolt. If you drop it down into the leg, of course, the gearcase has to come off and tipped over to dump out the screw!
Sometimes they go together with no trouble at all. (Sometimes not.)