I think the easiest way to go would be to create your threats and themes based on the chase and linking them to an organization, without linking them to a specific location. Every time your characters change to a new setting, you can decide, either by yourself or as a group, which of those threats and themes will be present, and if it has a unique threat that they want to conquer. Within the new setting, there are your usual locations, as you would have in any regular city creation. Give the threats you have decided on for this particular town a place to stay, either generic, if you can't think of anything cool, or a specifically cool idea you come up with. You can have a fixed face for a chase threat that will always show up. Like Col. Decker, to stay on the A-Team idea. Other times it might just be a faceless organization drone that is just chasing them because they are ordered to do so.
Basically: flesh out a new city each time the players are forced to go to a new setting. Doesn't have to be anything fancy, but if you have a cool idea, you can add it there and then.
Depending on what you want to focus on, you could put up a sort if investigation track, that will slowly fill up, every time the PCs stay in a place for too long. That will create some tension, when the time is running out to deal with the local problem, and they have to decide whether to let that threat run free, or to suffer the consequences of staying too long (losing a car, because it was discovered, for example). If you want to focus more on the local threats, you should give them as much time as they need.
Just because the characters don't have any of the major factions to call upon doesn't mean that the players can't use them for help. If there are enough factions looking for them, they might fight upon each other over who gets to take them, and the PCs can get away during the conflict.
And wyvern was faster, I was going to look for that thread as well.