Enjoy the pain. It means you're healing.
Seriously. I took a break in Service for a while and got lazy with civilian life. When I started
running again, it hurt like hell. The cause is that your lungs have been adapting the
entire time you've been smoking. (Analogs) Now that you've quit, they have to adapt
again. Just like the rest of your muscles. Stop doing push-ups for a week, then attempt
your max... your muscles will hurt like hell.
The other issue is that the "lining" of your lungs is started to heal. Just like when you
scrape yourself, or peel a sunburn, there's a layer of new skin which is VERY sensitive.
I would suggest not over-doing it at first. Take short, half-mile runs to begin with. Let
your leadership know that you've quit cigs and they'll probably be understanding about
it. At any rate, the point is to make sure you don't damage your lungs while they're
healing. Give them proper time to adjust and adapt. Without the intake of tar and the
like, your lung capacity is going to increase and you'll soon find that your 2-3 mile runs
will get easier now than they've ever been.