cake-- i would NOT do bootcamp, thats for sure! Very high impact exercises, prob.
I really dont know a whole lot about knee pain.... but i can PROMISE you that if you truly take a week or two OFF, COMPLETELY TOTALLY OFF (*light* jogging does not count as off) including bootcamp and anything else stressfull, that you will NOT LOSE any of your fitness. I know that now is not an ideal time to be needing to skip long runs, especially. Is it IT band? Have you tried foam rolling? Many peopl swear by this, but its not necessarily appropriate for all types of pain.
When it comes down to it, you could always take something, eh hem, STRONGER to get through your long runs. I will get in trouble for saying that, because medication only masks the pain, and doesnt solve the problem (and can make it worse, because you dont FEEL like i hurts, ya know?) Percocets and vicodan work well. And im not joking.
Cake, i know what it feels like to train SO HARD for such a seemingly unachievable goal. At this point, whats going through your mind is what you need to do to cross the finish line. I get that. Two of my marathons i was suffering stress fractures, one in my 2nd metatarsal, and the other near the top of my foot. Percocet got me across the finish line.
And my injuries have never fully healed.
Seriously, it MIGHT just be screaming from the overuse, and ramp up in mileage. TAKE ONE WEEK OFF-- NO RUNNING, NO JUMPING, no STRENGTH Training. Maybe yoga?

Seriously you Wont lose your fitness.
Jamsk8r-- to Boston qualify i need to run a certified marathon in UNDER 3 hours and 40 minuts. Thats it... maintain a pace of approx 8:20 per mile or faster, for 26.2 miles, and i am in.

Easier said than done. But i know i can, i just have to train for it.
Unfortunately, i am DONE running, even recreationally, for an undetermined amount of time. I dont want to hate running. It brings me joy, and currently, it is joyless. Of course, the fact that i am about 4 % body fat ABOVE my ideal, racing BF range might be playing a part in not enjoying running