How do I move past hurdle in training my body to run??

Months back I started the Couch to 5K Program and got half way through week 3 when I sprained my ankle. I took a little time off to heal and then started again at week 2. I completed week 2 and week 3 (twice) but ended up having surgery that required me not to exercise for 6 weeks. Today I did day 2 of week 3, but I still don't feel that I'll be ready to move to week 4 next week. Running 3 minutes straight still feels difficult to me, so how will I be able to run 5 minutes straight? How do I mentally push myself to run 5 minutes straight? I try to mentally motivate myself, but I just can't get past the 3 minutes. Should I stay at week 3 for a couple weeks to increase my lung capacity (I was a smoker for 9 years and have quit off and on this year, currently on day 7 of no smoking), or should I force myself to attempt week 4?