Cody...
Get a metric bolt the same size and thread as your axle, i forget what size it is i would have to go grab one of mine and measure it to tell you for sure. The local Runnings Farm and Fleet here has them, along with any other farm supply stores or good hardware stores with metric bolts in the little plastic bins.
Now buy that bolt and a matching nut, only a few bucks each, put the nut on the bolt and spin down to the head end, now that you have the bolt take it to a bench grinder and hold it at a 45 degree angle and grind around the end to create kind of a dull pencil like point on it, just putting a 45 degree chamfer on the end of the bolt and leaving the very end flat to push on the crankshaft. After you get that done put the head in a vise and then grab a wrench and spin the nut back off, it will clean up the threads on the end of the bolt where you ground into them, you can use a thread die to if you have a large metric tap and die set, most of us don't. now after the nut is off spin it into the flywheel until its hand tight then get a wrench that fits the bolt and a rubber mallet, put the wrench on the bolt and just hold the end of the wrench on the bolt head and smack the wrench hard and fast with the rubber mallet a few times, yes the flywheel will turn, but usually a few shocks of the rubber mallet will pop it off unless it was sitting open somewhere and rusting for a while. If its rusted on lay the motor on its side, flywheel up, and fill the center hole where you are screwing in that bolt of the flywheel with PB Blaster and let it soak overnight and try it again.
I don't have an impact wrench but if you have one that would substitute for the wrench and mallet. I get them off ALL THE TIME using this method. I have bolts that are ground down like this and one thats not for those that need a larger flat surface on the end. I even took one bolt and put it in a vise on my drill press and drilled through the center to eventually thread it and make my own puller, but the bolt and shock method always takes them off anyway.
If you get bad threads in the center of the flywheel it won't affect anything other than your ability to remove it, they are there for the puller only. And you can always buy a large metric tap to clean up the flywheel threads.
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1984 Honda ATC200ES "Big Red"
1982 ATC200E "Hondie"
1988 TRX300FW "Project Quad" Still in progress....