<human>: Give me a shortened version of the text

I've been lurking for awhile now and I've decided to post because I have some questions and want some attention.  I've been running now for about 3 weeks on the C25k program. I've been a smoker for about 6 years now and I quit completely when I started C25k. When I started, i couldn't run 90 seconds without practically wheezing. 
 After the 3 weeks, 3 minutes was going smoother and smoother each time. Well, that's when my knee started to do this weird popping thing while I was at work(I stock groceries overnight. requires a lot of bending down and what not).  The popping didn't necessarily hurt, it just felt like my knee really needed to pop.  I kept running on it until it actually started to hurt when i bent down at work. It never seemed to bother me when i was running.  So i took about 10 days off from running.  Today I started back and man... It was rough. I thought I could jump back into it a little behind but catch up quickly. The 3 minute run was a killer.
I was running about 5-6 times a week before my knee incident.  My biggest problem was that my lungs would feel like they were on fire. This first run after my hiatus, my calves were the real killer.

23--male--6'4--205lbs--been 10 years since I've ran over a mile at a time

So my questions are:

When do your lungs allow you to run further?

Am I doing anything wrong that you can see?

Do I just need to tough it out until my body adjusts to the torment I'm putting it through?
<bot>: 6yrs smoker, C25k program, 3 weeks in, stopped because of knee. Started back after 10 days, and i feel like death.