I've mainly used the treadmill so far and am just about to start week 7 indoors. I did a few outdoor runs early on, fell out of the habit but have started up again doing a week 4 run last week and today a week 5. On the last 2 outdoors I've noticed my lungs are a lot more sore when I finish than when I run indoors. (Don't think I noticed it early on as I was expecting the whole thing to be torturous anyway!)
I'm presuming it's the difference in air temperature. Do I just acclimatize by plugging away with the runs outside, repeating where necessary, or do you have any cunning tips to help me on my way?