You need the proper size die. Get a caliper (vernier or digital) and a thread pitch gauge to determine what thread is on there. Once you have the thread (diameter and pitch), get the appropriate die to clean up the threads.
I'm guessing though that the threads are going to be beyond repair if you've used other dies on it. You're next option is to machine the end of the shaft down and use a smaller die to cut a new thread, then get a matching nut. The problem with this is the shaft is most likely heat treated (hardened, which is why you had trouble already) so if you machine the shaft down, you'll lose the hardness and probably end up with shaft failure down the road.
Another option is to weld the flywheel on, but unless you or somebody you know is a VERY skilled welder, I wouldn't recommend this. Welding + crankshafts = unbalanced crank = engine disaster.