Hard to diagnose a noise without hearing it.
Some info:
The primary chain connected the crankshaft to the trans. The 550 has no tensioner there. So, with a bit of wear there is slack to be taken up on one side of the chain or the other, depending on relative speed between crank a trans shafts. If the speeds change the slack side changes.
For this reason it is best to have all the cylinders firing at the same strength, in order for the crank to spin at a consistent speed. A weak cylinder will change the crank speed and make the chain "whip" as the slack moves from top to bottom and back.
Also with the crank's speed changes, is gear train "clack" in the trans as the gear tooth contact changes from front side to back side of the gear teeth. When all these bits are under a load is when the parts are the quietest.
One thing to minimized primary chain noise and gear train "clack" at idle is to be sure the cylinders are all firing evenly. On a good engine with all bit working, this is achieved by a vacuum carb sync.
Carb vacuum sync is preceded by a complete tune up, Valve adjust, cam chain adjust, Spark plugs cleaned or renewed and gaped, points cleaned/renewed gaped an timed, and the air filter cleaned as new or renewed.
If you still have a cold head pipe after the above is addressed, and the compression is similar to other working cylinders, then spark is verified to the cold cylinder. After that, it is a carb issue feeding improper mixture to the cold cylinder, possibly due to a pilot jet blockage.