I've pulled the plugs (they look perfect, replaced less than 100 miles ago) and turned the engine over by hand, and can't feel anything out of order, or hear anything odd. I checked the crank, via the spark plug hole + graduated stick method, and it appears to be straight. Pulled the valve cover, valves were about as tight as I expected them to be, clearances were on the low side, but still within spec. Opened them back up to the higher end, no change in knocking sound. Left side engine cover is now off, old stator was affixed inside the cover perfectly, no loose bolts, so signs of any metal to metal contact. Engine oil is still very clean, no signs of metal. I've taken this opportunity to install the Electrosport stator I've had laying around, and fuss with the electrical system a bit.
Any ideas on the knock? How do I go about checking the starter clutch? This is my best guess, as I don't think an actual rod knock would develop so quickly, or without any sort of warning. I've never had any problems with the transmission clutch, and don't expect it to be the culprit with 16k miles. I can't feel the knock through the foot pegs with normal street shoes on, and I can only feel it slightly with my bare hand on the engine case, or on the stator cover. I'm going to go back to spinning wrenches, and I'll let you guys know how it turns out.
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