I still think that the variator nut wasn't torqued down properly at some point, or the parts weren't assembled properly on the crank.
An OEM crank from KYMCO is $133.98 from Stadium Yamaha. That, a starter bendix, and a drive face will get you back on the street parts wise. I'm actually in the process of rebuilding a very similar engine at the moment. It's a Chinese QMB139, but a lot of the parts are the same. I wish you were closer, I'd invite you over to help.
Yes, you can reposition the drive face on the crank, but you'll need a new drive face. The splines are gone from the inside diameter of the drive face (that's the pulley half with the teeth on it). Though you could technically get away with doing that, I would advise against it.
The hardest part of rebuilding a 4-stroke engine for a lot of people is understanding the engine timing, and setting it up right. It's not very hard though, and there are timing marks on the parts to show how they go. Don't be too intimidated about replacing the crank - we're here to help, and replacing the crank is the correct way to fix the damage. With the crankshaft being as it is, the trust is gone, and I don't feel like it's a good idea to re-use the parts you have. Without the splines on the crank, and on the drive face it's going to be very easy to assemble the parts "off center" causing excessive engine vibration, premature belt wear, and things of that nature.
Now, all that said, if you do re-use the old parts, I don't suppose you're going to damage things too much worse than they already are, but I'd grab a spare belt, and get the parts for the job anyway.
~Josh