I had the same problem. I opted to remove the propeller, hoist the engine a few feet, then remove the shaft by pulling it forward into the cabin. After that, removing it with a gear puller was a cinch, and nothing broke.
Not sure if you can remove the shaft by pulling it aft on your boat so it clears the rudder (assuming you get the coupling off). Servicing the whole shaft assembly is certainly easier when it's completely out. Replacing the cutlass bearing, shaft seal, even inspecting the shaft for scoring is better done with the shaft out. It only took me an hour to completely disconnect the engine, raise it, and get the shaft out. It'll likely take the same to get it back in, and I get to refamiliarize myself with all the wiring again. Fun.
Let us know how it goes.