I'm no expert, but I'd suggest you try repeating week 3 day 1. See how you feel during/after the run. Make sure you spend enough time warming up and cooling down as well as stretching. If you have pain, stop and walk.
What you do from there is based on how you feel. If you feel like week 3 is way to hard, try going back to week 2. I don't think you'll have to start over completely, but you don't want to reinjure yourself either, so take it a little easier the first few times out there.