Nothing was on top of the lower shift shaft when I dropped the lower unit of a '93 90hp Mariner and nothing fell out to my knowledge. I recall(boat's at the lake) seeing the splines of the upper shift shaft in the upper unit and wondering how the two mated. Is the coupler in the upper unit somewhere?
I'm having trouble reconciling the manual's illustration with what I saw. Instead of the manual's shift shaft retainer and bushing, for example, which seem to be bolted to top of lower unit, I just have a hard plastic donut on the lower shift shaft.