The pieces could have come through the reeds. When disassembling the engine it will become clear where they came from, outside or inside. If they come from outside the engine there is not much to do. Byt where they come from is not my main concern right now. Now I'm trying to figure out the other problems (2 and 3).

I've tried to measure the the cylinder height but having only a vernier caliper dosn't make the measurement as precise as I want to. They are somewhere around 86 mm.
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MC21, GP-Replica (Daijiro Kato, Telefonica Movistar Team 2001)