Sounds like when you put the 2 halves back together, you didnt get the 2 gear shifting shafts to mate up correctly. The "shoe" on the lower end of the top shaft has to sit over the upperend of the lower shaft.
If they are not properly aligned, I guess you have to disassemble it again and put it back together correctly.
Lower the bottom section put the boat in forward gear with the shifter the shift shoe should point straight forward.Turn the shift foot forward while turning the propshaft counterclock wise.Reassemble and align the splines by turning the propshaft counter clockwise only,Turning it clockwise will take it out of forward gear.