Shaft seems fine, just the flywheel that's buggered up. I was concerned about stripping threads, anyone have torque specs for the flywheel off the top of they're head?If the shaft and the flywheel is all bugger up like you say you are never going to get the matting surface to hold friction. It is a tapered shaft with tight tolerance, not going to work if it is not matching taper and clean. Then you can tighten nut to proper tourqe. Those threads will only stretch so much and be worried tourqe to much you might strip them.
If you get a new flywheel, work on the shaft to match taper and get it clean.
Edit: just found the specs, 28nm, roughly 20 ft lbs.