Are you having a reaction to protein? Well, yeah, but it's a natural one - you're body is telling you (ok, screaming is more like it) that your diet is out of balance and it doesn't like it. And yes, as a runner, you do need more carbs. Think of it this way: Protein = building muscle, Carbs = fuel for muscles.
Running requires fuel. Weightlifting requires protein. Both require healthy diets w/ decent amounts of all your basic foods groups (even sugar).

If your goal is to build muscle and be more toned, ideally you should cut back on the running and up your time w/ the weights. You should NOT, however, completely stop running altogether. You should also NOT throw a healthy diet of appropriate proportions of carbs & protein out the window in the hopes that it will magically transform your body into any shape or form. No matter how many meals you eat a day, if your dietary proportions are whacked you are going to feel it. And being the "moderation maniac" that I am, I'll even go as far as to tell you that if this diet does magically transform you, you likely didn't achieve that body in a healthy manner and you're probably not going to reap long-term benefits from it either.

But then, I'm of the "hippie" class that teaches, "If it's hurting like that, it was a DUMB IDEA to do it!" Er.... I mean, "Listen to what you're body is telling you (within knowledgeable limits, of course)."

------------------
Cheers! ~ Evin
My User Profile[/URL" target="_blank">

You're eating clean for a sedentary lifestyle. I dont want to say DUH, but geesh.

Basically I only eat fish or meat and I drink water. When I started Atkins about 3-4 years ago you feel kind of weak (or even sick) as your body uses up the glycogen and goes to fat burning. That's why you do the first 2 week intro.

I run about 35 miles a week and do it on my no-carb diet. I am also 5'9" and weigh about 133 right now.

You might want to check out Chris Carmichael's "Food For Fitness"
There is a great chapter in it about low carb and endurance athletes.
He basically states that low carb diets are not for runners and other endurance athletes.
He also explains how to eat at different stages of training ie: base, peak, taper, etc. (Carmichael is/was Lance Armstrong's coach and runs Carmichael Training Systems)