Take the flywheel back off, go to the parts house and get some valve lapping compound, put it on the crankshaft taper and on the inside taper of the flywheel, then install the flywheel back on the crank by hand. Now take the flywheel and turn it back and forth, this is going to take a bit of work because obviously its way out of whack.
Keep doing this removing the flywheel wiping it off and checking progress till you have full contact between the flywheel and crankshaft. You can look at the surface of the crank and inside of the flywheel for clues how much more needs to be done. When you are done bot the crankshaft and the inside of the flywheel should have a nice dull machined looking finish to them.
Make sure to get both surfaces spotlessly clean , I recommend brake cleaner for this, then reinstall the flywheel with a new key and torque it to spec, that should solve your issues.