FWIW here's my diagnosis:I wish I could say there was a magic fix to this problem but all I really did is remove the ignition components test them and put it back together.....
....The idle likes to creep up on it's own and it's not the carbs so I am wondering if it's staying advancd and the engine revs a little. It's idles back down to normal about 10 seconds after I stop at a light.
Your removal and refitting of the ignition components has resulted in the system obtaining a more reliable grounding -- if it was my machine, I'd still fit a ground cable between the coil/condenser bracket bolt to the top engine hanger bolt, just to be sure about it not conking out again.
The top end rattle is probably the cam-sprocket rivets or slack/broken advancer springs, as we (you & I so far) have previously guessed -- this, I reckon, would account for
- a) the variation in ignition timing, and
b) the idle speed's reluctance to settle immediately