I also suffer from knee pain - Runner's Knee I think. My knee "went" one day when I was out running and it's never been the same since (it always feels much weaker than the other knee).
I've seen numerous physios who have all said it's not the knee specifically causing the problem, it's the whole body - my core. I had never really thought about toning my core muscles - I thought by running I would automatically lose any weight around my middle. I did, but my leg muscles were far stronger than any other muscles, and the more I ran, the more I needed to have a strong core to support this.
So - long story short. I'd recommend starting Pilates, working really hard to strengthen your core to support your legs when you're running. I also now do yoga once a week to stretch everything out which I find really helps.
Also try all over weights (i.e a body pump class). I think a lot of women especially start running without actually having the body for it! Which can cause injuries and problems.
Good luck! I started re-strengthening my body back in August (Pilates, yoga and weights) and my knee improved so much I was up running half marathons and training for the London Marathon (which I have had to pull out of for separate reasons - but at least my knee was going ok!).
Sounds like Runner's Knee. Do LOADS of stretches before you run. Literally every stretch you can think of - quads, hamstrings, calves, hips etc. I sometimes get it and the pain is enough to make me have to stop running. I started doing 20mins of yoga before my runs to warm the muscles up and that seems to help.
I had a Piriformis problem for about six months a few years back. Started stretching properly before and after my runs, also took up yoga and then after a while it just went away!! I still get the odd twinge after running but stretching really is the key!
I think it depends what you are hoping to achieve from the marathon. I'm a novice runner and was training well up til early Jan when I got the flu followed by Thyroiditis which pretty much scuppered my training for at least a month.
I've recently been told the thyroid problem is now normal and am feeling great. Sorely tempted to give the marathon a go despite knowing the sensible option would be to defer.
I reckon I could slog it round with a bit of walking in between, but the question is what would be more painful for me - getting a rubbish time and the chance of dropping out due to lack of fitness, or not trying at all and feeling miserable when watching it from the sidelines.