I don't necessarily think that chronic hypoglycemia explains the muscle pain etc. But if you look at fibromyalgia and other complaints, pain and fatigue seem to go together a lot of the time.

I'm bipolar. A common observation with depression is low energy, also an increased perception of pain. I find these things run together for me. I have a chronic shoulder pain issue with an obvious cause, I fell down in the mud somewhere around 10 years ago, onto a hard metal object. Since then that shoulder acts up now and again. If I'm in hypo or frank mania, the shoulder hurts less--in fact it doesn't hurt at all. If I'm down, it tends to be worse. All of this got better when I went from a looser low carb diet to a more intentional ketogenic diet.

Another pain/fatigue connection is caffeine. I cycle on and off the stuff--it gives me a boost and makes my shoulder feel good, but only if I'm sensitive to it. So I'll cycle down, maybe taking the odd aspirin to work out, and then bring it back up again slowly, until it loses effect again.

Ketosis also seems to increase my sensitivity to caffeine, if I go from a less ketogenic to a more ketogenic diet, or if I fast for a day, often I'll have to cut back on the caffeine to avoid becoming jittery.

I'm not saying you should use caffeine to manage your energy levels.
Just something to consider if your pattern of intake has changed with the diet change.