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You know what I think , it sounds to me like the Auto-Decompressor is what is ticking/rattling , maybe check the spring , and make sure the setup is free and moves but goes back into place , check the pin for damage , etc. ... otherwise I would suggest checking valve clearance , but from your description , you have already done that along with a complete tear down ...but my first thought is Decompressor or a "valve Train" issue , which includes chain , tensioner , cam ,buckets , decompressor , but it definitely sounds like its in the valve train somewhere , sorry can't give a more enlightening reply , but I find it odd , as I am sure you do , that such a low hour bike would start making noises out of the blue like that .......
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