My knees were busted too. Took me a while to realize I was overtraining at the beginning. The ramp up to 5k took me 10 weeks when it should have taken 8 as I was all sorts of busted up after thinking I could just complete the goal early. I was wrong. Slow and steady won that race and every race after that in my experience. Injured myself a few more times on the way to 10k and again on the way to 21.
I seem to have leveled out so next year's goal is 42.2 for a full marathon distance.