Do you recall how many threads were exposed when the fywheel was in its original (un-disassembled) state?
If when the nut was fully tightened you had several threads exposed you can fix it easily.
Just carefully grind off ONLY the stripped thread and run a die down the threads. Then bring it back up the shaft to within a couple of threads of the end and square the end of the shaft with a file. SLIGHTLY knock the edge off the first thread and yer back in buisiness.
The fun part will probably be finding a die in the same thread as the shaft. They can be hard to find in larger thread sizes outside of dedicated "tools only" shops.