Is the pain on the inside back of the knee? or outside? or both?!

I think if your fitness is good (which i suspect you are ahead of most people training for the FLM!) I would advise giving it a longer rest period. Maybe 2 weeks without running? Try some cycling/cross training etc to keep fitness up.

In the mean time keep the icing up, 3 times a day 15 mins at a time.
Stretch quads, hams and calves also three times a day holding 20 seconds each.
Have you had new trainers recently? If you've been doing a lot of miles the cushioning in your trainers may have gone, this means less shock absorbtion. Or the same if you wear orthotics? or maybe you need some? have you had your foot position assessed?

Hope this helps....let me know exactly where the pain is, it might help me or others help you out more!

Heidi