Stretching and Tapering
I got that same knee pain in the beginning, when I over-stretched before a run, while my muscles were stiff and cold. At that time I had to stop and stretch in the middle of my runs, just to be able to finish 7 miles. After about three weeks of brisk walking instead of running, the pain went away. Now that my mileage is up, I don't find that I need to stretch any more, but I do make sure I take a long time to warm up (slow walk) before I even try to slow jog, and then hill sprint. The longer I take to warm up the faster and farther I can run, now.
Also, make sure you taper off a week or even two before the marathon. It will feel like you are getting out of shape, but you will find that you perform better during the marathon if you've given your muscles a rest just prior.
PS: I have only done 10k's and half's, and they are alot of fun. My first 10K almost killed me with blisters, but I got some good socks and have not had that problem again.
Chuck