As you initially note, primary drive is normally the location of this noise but the chains don't actually wear much and so are not the highest on a list of things to firstly check through. Gearbox and clutch rotating inertia are remote from crankshaft but linked through the primary chain, any significant oscillation from crankshaft speed changes have to also speed up and slow down the whole gearbox rotating mass via the chain which results in noise if all parts are not working in harmony.
Additional to above thread input, when you check timing have you got as close a match for cylinders 2&3 to 1&4 as possible? You may have to compromise (within reasonable small amounts) the points gap of 2&3 to refine this pairing and so reduce initial differentiation in crankshaft pulses.
Also, carb synchronisation is principally to get the slides to match for whole range operation in parity not specifically for tickover speed. A by product of this set well is smoothness at any rpm in comparison to wrongly set sync, but adjustment is ultimately too course to finely resolve low speed running.
Honda put in their manual a specific routine to adjust low speed running. After setting all the other items listed in this thread, then with motor warmed and idling pick one carb and turn the low speed mixture screw (it's fuel on pd carbs not air, also backwards compared to previous carbs with screwing in to lean and out to rich direction) inward to hear the engine acceleration to highest point (if you go too far it'll start to miss on that cylinder) and then from that peak rpm make it richer to bring the rpm down by 100 rpm. Then reset the overall tickover speed and repeat the routine for each subsequent cylinder until you've got setting for all four.
This trims the combustion for each cylinder to give essentially the same energy burn regardless of equipment variance to keep crankshaft pulses in equilibrium, and how the factory set them. They also note to record the final position as datum for future reference.
This should give the most smoothness for the engine as it is running with current equipment.