The PD carbs have a choke knob, and the cable moves the choke plates AND a fast idle cam. While the fast idle cam is engaged, the large idle knob doesn't do anything. As mentioned, there is a separate fast idle speed adjust screw.
You should get the K3 Honda Shop manual addendum, which has information about the PD carbs. (Chapter 19)
The 71 exhaust has less back pressure than the Stock 77-78 K3 exhaust, but it is way closer than an open pipe. These bikes were finely tuned to please the EPA. The higher back pressure of exhaust allowed the carbs to be set leaner and put less hydrocarbons out the exhaust. Lowering back pressure makes it run leaner, and run hotter. It may be possible to fix the idle with the idle mixture screw, turn them out some. This should also help the the pick up response off idle when opening the throttle, too.
In theory, there should be some tweaks to the slide needle and main jet, too. An A/F map made with a dyno would be the best indicator. But, you could also read spark plug deposits after power testing ("plug chops") to infer mixtures at different power settings. Got a test track?
Are you using the paper air filter?
To state the obvious. The stock (book value) carb settings and adjustment positions only apply to bikes in stock configuration.
I believe the factory glue on the air box was an installation aid for factory line workers, rather than a requirement. Clearly it should not leak air, though. If you are comfortable with the air seal, it should be fine. I never worried about it in my bikes.
Cheers,