there is a key in the shaft, make sure that it goes back in and you will be fine. you will not mess up the timing unless you mess with the optical sensor which is next to the stator. check the magnets on the flywheel to make sure they are loose and ready to fall off.
You will need an impact wrench and flywheel puller to get it off. Don't try to tap it off, thats how magnets get loose.