Quick release tight on front and back wheel.
Mavic Ksyriums can make noise where the spokes meet the hubs.
Shifters or cables moving around.
Stem bolts tight.
Headset.
Pedals tight.
Bottom bracket.
Seat post moving inside frame and noise is telegraphing. (Just spent a day trying to find and fix this on my new to me Supersix)
Seat rails moving in seat shell.
Void in weld at bottom bracket to seat tube junction that eventually cracked. (Very unlikely)
I know you have checked several of these. I listed them all since I have seen them at one time or another.