Listen to your body, it's trying to tell you something. You're body is not your enemy, it is the physical manifestation of every thought and feeling you have ever had. Listen to how hard you are being on yourself, it almost sounds like self hate. It's no wonder why you're feeling pain.
You are not going to get fat by treating your body with the love, respect, and giving it the occasional rest it deserves. The stress you're experiencing from your rigid exercise program, and poor body image, will slow down your metabolism, encouraging weight gain faster than taking a couple of days off a week. When you love your body, it loves you back. If you keep plowing thru your pain you're really going to injure yourself to the point of not being able to exercise for months. Then you're really going to panic.
I'm telling you this because I've been there. I've been a long distance runner for the last fifteen years. I've had many injuries over the years. At one point in my life, I hurt myself so badly by running thru the pain, I couldn't even walk for months. It was a lower back injury that made it impossible to even sit up for the first month. It well over a year before I could run a mile again. I learned the hard way.
There is a message in every ache and pain we feel. We have to have the good sense to learn to listen.
If you decided to take a week off to really give it a good rest. You'll only come back a stronger runner.
Now, I never run more than five or six miles, five times a week. I'm a much stronger runner than when I felt I had to be out there everyday. It's a much more enjoyable experience.
I also do yoga five days a week, and work with light weights a few days. In my best running only shape I weighed 128 pounds. Doing the weights and yoga I'm now 112, without any effort.
Let your mantra be "I love myself, and respect and honor my body. It holds a deeper wisdom than my ego".
BTW, how much sugar do you eat? It can really intensify pain and stiffness.