You drop/install a lower unit every time you change water pumps. I do my Yam 250 alone and the shifter splined shaft, pitot tube, and drive shaft must be aligned. It literally falls into place when correct. Run it on the hose and shift from f-n-r to be sure. It's definately not something a shop has to do. I use anti seize on bolt threads, rubber boot, and split line at assembly. Make sure it's full of gear oil...
