The clunky click could just be the transmission, maybe sort of out of gear, but slightly catching, if your shift cables are out of adjustment. The transmissions do a lot of clunking while shifting, etc, but they are STRONG.
I would imagine your main seals are about ready to quit doing their job. Possibly dried up, and leaking a little. You might also test your compression. if you are hearing a higher pitched clacking, you may have lost a ring. I don't think that jet from treats will fit your carburetor. Try calling Matt, at Motorwest. He probably has every jet option there. It's best to call them, and they have more than their website shows listed.
You can also ask him questions, as he's very keen on these bikes. I too love your large brake hubs! I think you can get replacement connections for those airboxes at Rinky Toys, but he's overseas.
That airbox, etc, shouldn't be your problem though. It's even possible you are getting an vacuum lock in your fuel line. If your cap isn't breathing well, it will starve it for fuel. My wife's bike had that issue for 3 years before I finally figured it out.
I like spark plugs: NGK B6HS or B7HS. also I run Amsoil Injector 2 stroke synthetic oil in my fuel at 3 oz. per gallon. (Yes, amsoil suggests other types of their oil for mopeds, but I have used most all of them, and the Injector just seems to run the best. I think it has to do with it's thickness somewhat.) Anyway, i also use that oil straight, in my transmission. Quieter shifting, cooler running, and just all around better than 30wt or whatever.