Thanks, that's very helpful. Did you have to dry dock it to deal with the shaft?
No, I did this in the water. Depending on the boat, the shaft only needs to be pushed back far enough to allow the transmission to clear the coupling. In my case that was about 2". The coupler was left on the shaft.
If you have the typical packing gland and nut, loosen the nuts, slide the shaft back, and tighten the nuts to stop the leaking water.
If you have a PSS shaft seal, basically the same process, loosen the collar, slide it back and tighten the collar again. Initially this leaked, by fiddling with the seal and moving the shaft I found a position where it did not leak. Replace the set screws with new cup point screws using blue locktite.
Full disclosure, I did not spend my youth under the hood of a car. Few would call me mechanically inclined. This is why we have credit cards and garages with real mechanics. However, in my neck of the woods good marine mechanics are few and far between, so I dove into this project on my own. A few things I learned:
Make sure your bilge pump and float switch work.
Don't move the lower motor mount nuts. If you do, you will have to realign the shaft. If you have a shaft seal this means that it will not seal until the motor is in pretty good alignment.
Be prepared to invest in wrenches you don't already have. In order to reach a couple of bolts it was necessary to bend one wrench into a curve, buy a stubby 12mm wrench (yours may vary), and buy a combination open end/box end ratcheting wrench with a pivoting head.
Replace the damper plate. It may not need to be replaced today, but it will eventually need replacing. It is unlikely that you will want to remove the transmission later to replace it. And according to the transmission guy, once it starts to fail it will take the transmission with it.