Fast travel is free inside provinces you control, you can increase your number of beacons through Land Races to a max of 5. You increase your flairs through Air Races.
As for replenishing them, look on the map for the circle with a downward arrow inside and a flair symbol. Normally they both come together.
The cool down timers can also be first halved then abolished completely with upgrades from the relevant challenges.
mrbenjamin's comments