i have the flywheel measured to be roughly 5-3/4" x 2-1/2" with about 1/2-5/8" clearance between it and the starter clutch gear.
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With pullers, the closer your attachment points are to the fitted/shrunk on section, the more efficient they are. This is why the original arrangement, with the plate-type puller, is the O.E.M. suggested method. But with the broken-off stud, a plate puller cannot be used. But maybe so........
Another idea. Again, I have no personal experience, just going by the photos and the Clymer manual.
The photos of the flywheel show 6 equidistant holes thru the outer diameter of the wheel (I suppose for lightening purposes?) - are these holes accessible from the back? i.e.,
"with about 1/2"-5/8" clearance"
It looks like they are. Page 141 of the Clymer, figure 41, shows the back of the flywheel with the starter clutch assembly still attached. The clutch assembly appears to be about 1/2" thick, which accounts for the clearance between the wheel and the clutch gear.
If this is correct, your'e back in business! Forget about a jaw-type puller, make yourself a heavy-duty plate type. This would involve making six pieces of steel plate, as thick as possible (1/2"-5/8") which can be slipped behind the flywheel, inline with the holes. Each plate has a tapped hole in it, using the largest diameter posible(looks like 1/2"?) Instead of making plates, you may be able to use heavy-wall nuts, if there is enough room to slip these in. But plates would be better - more contact area.
With these in place, now you have attachment points for your hardened puller bolts. Next you make a matching "backing" plate, out of 1/2" thick metal (the thicker the better), with 6 thru-holes, to match the diameter of the puller bolts. Because the flywheel holes are at the outer diameter of the wheel, the puller bolts/backing plate assembly has to be long enough to extend well beyond the outer face of the wheel,(to allow clearance for the flywheel, when it pops off) and the backing plate will consequently be of bigger diameter as well.
Now all that remains is a tapped hole, as large as possible (5/8"- 3/4"?), in the centre of the backing plate. Use a fine thread tap (and bolt of course), if possible. Less chance of pulling the threads out, when in use. Then assemble all to the flywheel, tighten as much as possible , and give the removal bolt a good whack. Tighten again, whack again, etc., until the flywheel pops. As mentioned previously,use heat, but as a last resort. A six-bolt plate puller should do the trick!
I realize all this fabrication, and the materials needed, may be beyond the capabililities of your own workshop, but this would all be "a snap" for any machine shop. I can't imagine the fabrication time being more than a couple hours. But this would save the cost of purchasing another jawed puller, which may not work.
Cheers, Miles