Just 2 days ago I had an 06 700 efi in the shop with the same problems. I ohmed the stator and it tested fine between the legs, but had continuity to ground. I pulled the cover, flywheel and the stator off. When I checked it again on the bench it didn't have continuity to ground anymore.
The cust had lubed his starter bendix in the past and what happened is when he tore it apart, one of the washers off the starter bendix had fallen out of place and was touching the wires, under the sheath, on the wiring right where the wires are connected to the coil wires) It was grounding out and not charging.
It's worth checking out. maybe you'll get lucky too.
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