I should give an update as well: after the piston exploded on my second engine, I filed another warranty claim and got a third. This time I was determined to do it differently, I split the cases, balanced the crank, replaced the bearings with Timkens, and surfaced the cylinder mating surface. I installed a meteor piston kit and was satisfied that this time, it would work. I was wrong. The rings snagged again, this time the exhaust and one of the transfers. I was mad to put it mildly. I wouldn't care if it was the stock piston, but those aftermarket kits cost 50 bucks.
I took a drill bit, wrapped it in sandpaper, and put it in an electric drill. I went inside the bore and held the bit parallel with the bore and moved the bit side to side across the offending ports. Now I will say that I didn't know if this would work or if I would ruin the coating, but it did work. I did it this way because hand sanding didn't do anything and I can't get a dremel in there at the correct angle to bevel it. I also don't recommend doing it this way.
I put a stock piston and rings in and now I'm worried about it breaking again and don't dare to ride it too far from my house.
Lesson learned: if you get a phantom cylinder, make 110% sure you get rid of sharp port edges, because they can snag from the factory.