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I've included this image to show how I've labelled all the pieces. I use paint sticks in different colors and Sharpies, plastic bags and tags to mark the heads, cylinders, camshafts, covers, etc. I note the RIGHT and LEFT sides and have a series of dash marks for the corresponding locations on reassembly. I also separate the two cylinders and heads and all the pieces so that I can't mix them up.
When most of the engine is disassembled like this it can get confusing with parts all over. But when everything is properly labelled it's like putting together a Ducati puzzle.