As the engine is warming up when I open the choke it starts making this strange clicking noise like once every 2 seconds or so, but only after I open the choke. Anyone know what this is?

 

If you are removing choke and the bike is not completely warm, it could be a lean misfire due to being cold. You hear the click as it not a complete backfire. Does the noise go away when the bike is completely up to temp? If so, its down to the cold blooded nature of Hondas. If it stays it could be tuned out with a pilot adjustment or synch of the carbs. Mechanically, there isn't much that could cause a two second interval click.