I have read over and over that it takes time for your body to adjust to using fat as fuel. So at first it will be really hard to run. Long distance running is not intense (as sprinting/weightlifting) so depending on how fast you need/want to lose the fat, you can just wait it out or start supplementing with carbs.
Try drinking more water - at least 1 gallon per day, take your vitamins and eat your veggies. If your muscles are sore, glutamine is a great supplement - 5-10g per day, in powder form. (It is really expensive! though I found several $55 bins in GNC that were on sale for $8 because they were cleaing out stock. make sure to check the expiry date)

I hike frequently on some very intense trails (heart rate goes up past 200) and have found that I perform better eating low carb, although initially it was not so.

Check out this site, it talks about nutrition for athletes, and explains why low carb (though higher than atkins induction) is better for athletes.. AND how it takes time to adapt for increased performance.

www.second-opinions.co.uk/athletic_diet.html