Glad you made it.
The best solution, in my opinion, remains the the slide hammer.

I know it`s in Romanian, but it has lots of photos and i`m sure you`ll understand what i say there.
It is a tutorial i wrote, about all the stages of total opening/dismantling the 3AJ engine:

Demontarea motorului de YAMAHA XT600Z TENERE 3 AJ- Yamaha Tenere - Motor

Somewhere there (pass the 3/4 of it) you will find the scheme and explanations of how to build an extractor for stubborn flywheels.
You will recognize those schemes as they are the only color schemes made with "Windows Paint", as all the other images from the tutorial are JPG`s.

If you won`t have all the patience in the world, these are the pictures that really say it :
http://www.tenereclub.ro/images/site...ja%20surub.jpg (the slide hammer)
http://www.tenereclub.ro/images/site...0presa%201.jpg (the assembly - slide hammer + the plate)

It is really important that the left end of the slide hammer (from the first link) to sit on this edge of the shaft (where the thread ends) and to have a cilinder profile, in order to cover the thread:
http://www.tenereclub.ro/images/site...ALONZO%201.jpg

If you build your own extractor using the scheme from the French manual (which i used only to inspire and don`t rely on 100%):
http://www.tenereclub.ro/images/site...20franceza.jpg
http://www.tenereclub.ro/images/site...20franceza.jpg
use thicker metal for the "plate" - 1 cm. I also did it from 2 pieces, welded with gas (argon):
http://www.tenereclub.ro/images/site...20-%20disc.jpg

If you still want to use the French extractor (sold also by some other shops on the internet), never place the long, extracting central screw directly on the shaft as you have all the chances to "flower" its axle like in the picture above.
http://www.tenereclub.ro/images/site...LONZZO%202.jpg

Also, very important is not to put heat in that area as the flywheel`s magneto is glued with epoxidic resins that will 100% fail under heat and leave you with a useless/"magnetless" flywheel (i was almost on the point to do the same mistake).
The nut i extracted with air impact wrench.

So... P.S. :
- Sorry for my English.
- If there`s no way to understand the schemes and explanations from them, please tell me and i`ll translate this part of the tutorial.