Gordon, just to clarify, I think you are talking about two different things. Cb sells the "jet doctor" which raises the point under the air filter where idle air is drawn: http://www.cbperformance.com/catalog.asp?ProductID=1507
Then there is the "weber update kit" which changes the main jet discharge to a horizontal tube:http://www.cbperformance.com/catalog.asp?ProductID=508
The jet doctors are less than $20, the update kit is $140, and includes new accel. pump diaphragms and venturis and gaskets/O-rings.
Kelly, you can definitely open up one air bypass to bring the idle air up to snuff. I think it is a 7 or 8mm locknut, and then a stubby flat screwdriver to open it a bit. You should be able to adjust it while it is running with the snail in place. Make sure the snail is sealed real well, cause any air leak will cause it to read different in that cylinder. It is number one, isn't it, IIRC? This adjustment works for idle only, as soon as you crack the throttle air is no longer drawn through this orifice.
I agree with Gordon, if your air filters and bases are clean, and your fuel source is clean, the biggest problem is water in the carbs. You really need to address this on Speedsters, not an issue at all on Spyders. I like the smear of grease method, it works.
I would NOT make up a balance tube for a dual Weber setup. It is a waste of time, these things are not that hard to tune well, and then they should stay that way. All it would do is make it harder for you to set the individual idle mixtures/speeds, and MASK the problem, not solve it. The only exception to this is if you have EFI and a manifold air pressure(MAP) sensor. Otherwise, don't overcomplicate things. And fix your linkage to eliminate ALL play. Set it and forget it.
There is a slight possibility that your intake manifold gasket and/or carb-to-manifold gasket is leaking on that one cylinder slightly. You might want to check that out as I know you've had at least the right side carb off before.
The real solution to intake manifold leaks for me was Vanagon Waterboxer gaskets, port matched by hand cutting, Mr. Xacto knife is your friend. Use Loctite 517 anaerobic gasket maker on both sides, a very light smear on both sides of the gasket, along with their spray primer. You need thick steel washers on top of the manifold(one has to be ground into a D shape to fit), the 11mm STEEL manifold nuts(not brass), and thread locker. Or go like Gordon and go gasketless, I am not sure what he used there. DO NOT EVER use the CB gaskets, they are soft and will squish out and leak, guaranteed! Get the swivel thin-wall socket Gordon got, and torque them to 18-20 ft. lbs. Let them dry overnight, and say goodbye to manifold leaks.