Yeah, I know exactly what you mean. I mountain bike the ski trails at Killington (about 1.5 hr ride several times a week) and things are a *little* different for me with eating this way, but I do feel like they are getting better as my body settles into this way of eating. I can tell you for absolute certainty that when I did the first two weeks of induction, I hadn't bought a multivitamin for the first week and I felt like **it. I was barely able to muster up the energy to go for a walk. Then, I got my GNC multivitamins and feel 100% better. Atkins talks about losing electolytes during the big initial weight loss which will cause you to bonk. I am pretty sure this is why I felt so lethargic because my diet is clean. Also, with you being so active like you are, I would suspect that your eating needs to be a clean as possible to maximize what you get from everything that goes in your mouth.
As far as carb loading before a major workout. I have read in several places that discuss regimes for body builders where they cylce carbs in (ketogenic cycling diet). So that they get there enery for their workout and are still able to maximize fat loss through the use of the low carb diet. I understand the concept and I am sure that it works quite well for them, but.....
...you talked about reactive hypoglycemia which is why I chose to eat this way. I know that I am obese because I have no control over carbs or food when I ate the way I did previously (I suspect that the bodybuilders using the carb cycling have better control of their eating). I personally would not dream
of adding in any carbs to try to squeeze out an extra gain out of a workout. Here is my reasoning. I am very athletic, obese, but nontheless, athletic. If I were to try to add carbs back in for the purpose of gaining a better burn from a run or workout, I am, for one, not doing Atkins like prescribed (which so many people have been successful at) and two, I would be opening the door for potential cravings to come back and for me to possibly fall off plan. I think of it this way...when I am 150 lbs, I will be able to run, bike, hike, paddle, and climb like the wind.
I am at the end of my third week on Atkins. I have zero cravings, the weight is melting off of me with not one ounce of struggle, and I feel amazing. Atkins states in his book that the amount of weight you lose is *almost* directly proportional to the amount of carbs you eat up to a point. I am certainly not any kind of expert but I would suggest sticking to plan as prescribed and not trying to worry about getting extra gains out of your workouts at this point. You will see more gains in your running by getting the weight off.
PS. I know this is long winded, but I wanted to say that I was an Atkins nay-sayer, but I can't tell you how great I feel and how much I LOVE THIS PLAN. Did I mention how fantastic I feel?