My 77 550 F clunks, too. It is the trans.
The crankshaft is connected to the trans gear shaft via a primary chain. The 550s primary chain has no tensioner. So, without a load, the slack side of the chain alternates sides with changes in the crankshaft speeds. There's really not much of a flywheel to even out the crankshaft speed at idle, only the alternator rotor, and the mass of the trans gears, connected by that flopping primary chain.
The trans gear teeth are always engaged, even when the slider dogs don't lock them to the shaft they are on. If each cylinder doesn't fire with the exactly the same strength as the others, the crankshaft changes speed and the mass of the rotating components make the gear teeth make contact on alternate faces. This sounds like clunking or what I call gear train clack. You'll note that even at idle RPM, with the bike rolling and in gear, there will be no clunking/clack. The noise is reduced with the carbs synched and the ignition timing spot on the money for each point set. The idle air screws and tappet adjustments can also effect cylinder firing strength/evenness at idle.
You can isolate the source of your clunk with a screwdriver handle placed in the your ear socket and the tip used as a probe. The noise will be loudest at the source.
The front bake arm should pivot freely, with pads and the positioner bolt/spring removed. I suspect rust, or an assembly issue/error with the front fender and washers/spacers.
Cheers,