I was trying to remove the flywheel nut while providing resistance to the pto coupler, now if I spin the flywheel and provide resistance to the coupler the coupler remains in place while the flywheel (and pistons) rotate. When I spin the flywheel without resistance to the coupler they all spin normally.... Is it possible I damaged something? Yamaha 650 engine on a Boston Whaler Rage.
More than likely you've just backed the PTO sprocket off of the drive shaft of the PTO itself. I'd suspect if you dismount the PTO (if you can easily) from the engine, you'll be able to see what you'd need to do to fix it. Bottom line, if things gave way easily, there shouldn't be any damage, but you may have to put things back together again. Like I said, you'll have to take the PTO itself away from the engine before you'd be able to tell.