Which shaft are you talking about; prop shaft, input shaft, or vertical drive shaft? Either way, a broken spline warrants inspecting the engine coupler. If you already have the engine out for the retrofit, I'd replace the coupler now anyway so you're not going through this all over again if/when the coupler fails as a result of what seems to have been a pretty good impact. Having said that, it may have also been due to a badly corroded shaft. Finding out what caused the failure is important here as it will steer you in a specific diagnostic/repair direction so you cover the bases before putting everything back together again.
Do yourself a favour and replace all the regular maintenance items in the transom assy., including all the bellows, lower shift cable, intake hose, gear lube hose if applicable and the thru-transom fitting, gimbal bearing, etc. You should also check the condition of the seals and bushings in the gimbal ring for the shift shaft, and replace the trim limit/sender pucks assy. You're in there and now's the time while you have access, and it'll give you a record of when all those components were last changed. Nothing more frustrating than replacing the bellows, putting her in the water and finding that your trim gauge or limit don't work properly.
You should also try to tighten the nuts on the inner transom assembly plate, they should be tight. If you can keep turning them, you likely have a cored transom that is compromised and needs to be addressed before you do anything else as this would be a structural/safety issue.
Inspect the exhaust shutters and replace if needed. If they're missing, make sure they're not in the bottom of the exhaust horn. You can check the bottom of the horn from the outside where the exhaust bellows is installed.
Don't know what type of water she'll be in but I can stress enough the importance of ensuring you have the correct anodes in place and replace them as needed.
Keep up the good work.
er