don - one note on this: I've seen stuffing boxes and shafts replaced with the boat in the water a couple times.
we were down in the abacos and a guy did the whole thing. Basically disconnected the shaft and took the prop off. he then went down with a mask and a wood bung and pulled the shaft out (bung in place).
stuffing box was switched, bung pulled, and shaft put back in - finally adding the stuffing.
all done with minimal water in the boat.
just in case you are feeling daring...