On an '08, maybe 20 minutes if you have had the fairings off at least twice before; the first time getting into the bike might take a while fumbling around. A second generation C-14 will be a little different due to the glovebox change and the relay location (you have to remove the relay mount on an early but not on a 2nd gen. bike).
Yes, you have to remove the left / mid fairing to get to the air filter.
How dirty it is depends entirely on the conditions you ride in mostly. Lots of riding on gravel roads or through road construction will get a filter dirty much faster than riding on relatively clean roads. 5K miles is not much though unless you typically ride in sandstorms and the filter should not be very dirty yet.
I check mine when the fairings are coming off anyway for other maintenance; I will change the air filter, the anti- freeze and check the throttle body balance during the next maintenance cycle.
Brian
How long does it take to change the filter? Do you HAVE to pull bodywork? At 5k, I don't think mine is ready for a change, but wouldn't mind checking it out. Mine is a 2011.