Good point. If the ends of the clamps are touching it's too tight, they should have at least 2-3 mm of clearance between the ends. I have them around 3 mm roughly and I've taken the carbs off a bunch of times and I'm fine. Also keep in mind that as the bike warms up the idle will climb a bit. Best to adjust the idle when it is fully warmed up, at least 30 mins of riding. It could be that the bike is simply warming up and at that high idle rpm its just climbing naturally. You may be fine, but just slightly lean if it's stock and high on the standard idle.
I've never removed the airbox but the general consensus is they are a bit of a bitch to get out but doable. If you're going to completely can the airbox for pods I guess you could cut it out to make it easier.