I had a mystery noise in an engine (competition AJS 500 single) once and it took 3 or 4 tear downs, multiple head swaps etc to finally find it. When the engine first started up it sounded fine, but when it got to a specific temp a very loud clatter suddenly appeared. When engine was cooled down and started again it would come back when hot again. It would sound fine then the noise would come on like it had been switched on. Eventually i found it only after pulling the engine apart real quick while it was still warm and when the head was off i finally noticed that the cylinder sleeve made a click noise when pressed!. So what was happening was when the engine heated up the sleeve was comming loose and could move. It was not made/fitted correctly. It was a relief to finally find what the cause of the noise was.
A mechanics stethoscope is a very handy item to have as well, to pin point where noise is comming from. Pretty sure MCS has them.