I agree with having the joint pain looked into...
My son was older when diagnosed, 16-almost 17, so it may be a bit different??? Prior to being diagnosed, he was very fatigued. He somehow managed to 'attend' his regular activities but had a really tough time keeping up, would be exhausted and falling asleep very often as soon as he got home from school. At diagnosis, he was put on exclusive EN to induce remission (plus one week of IV flagyl), he responded very quickly and within 2-3 weeks was back full speed (it did take a bit more time to regain his muscle strength and endurance but the 'energy' was there).
In our experience, once the healing process took hold (even if it wasn't full remission yet), the fatigue went away.
Doctors didn't limit his activities.... he was to do as much as he felt he could.
Also keep in mind that the fatigue may be related to vitamin or mineral levels. If he is having any issues with absorption, he could be low in certain areas - David, Dusty or MLP may be able to give you advice re certain minerals/vitamins levels to have checked.
I'm not familiar with the SCD diet but, perhaps, you can add some of the (easily absorbed) nutritional shakes to his diet to boost his daily nutrition.