No marks on top of piston at all what so ever. Not missing circlips, pins, skirts, etc. Which leads me to come to these conclusions:
1: The ski was brought to a SHI#@$Y dealership, and tore apart a perfect good motor to try and screw the customer? Maybe offer hime $400 bucks for the whole works because it is "blown up." This seems friggin crazy, but it's definitely a possiblity. Are heads serial numbered to match the block? I found some casting numbers but nothing that matches. Is there anyway to determine if this is even the proper head for the motor.
(1997 Yamaha GP1200)
I don't think heads match the block. Is there a part number stamped on the head? A quick search within an online parts site for Yammie would answer that question.
2: A main bearing cage, rod bearing, piece of casting, managed to make its way from the bottom end, up into the cylinder where it was mashed into the cylinder head without causing any damage to piston or cylinder.
With that much damage to the head there WOULD be damage to the piston Dome. No if's and's or but's. The scoring you found on the cylinder wall could be water scoring (quite possible since it was a jetski motor) and that would explain why a hone would fix that.
3: Something was sucked in through the intake, and shot right back out.
Not likely. There was too much damage to the head to just be sucked out into the exhuast that quick. What ever it was bounced around a while before being either burnt to nothing or sent out the exhaust port.
Even with these possiblities, one thing just doesn't make sense to me. If the head was damaged that bad, something forcing chunks of metal into the dome, then where is the force doing that work? It simply does not add up to me.