Congratulations on your success with the SCD diet. I have been on the diet for 7 years and healed two rectal fistulas and have been in complete remission without one flare or pain since 2007. The only drug I take is pentassa 1000mg 3x day. This is a very mild drug with no side effects like humira or remicade or 6mp.
The SCD diet seems to work best in people with UC or people with CD in the colon, and not so good for people with CD and inflammation in the illium. If you never had surgery before, you don't have scar tissue, so that is not your problem.
It sounds to me that you have some minor CD inflammation going on in your small intestine, probably in your illium. I would go to your GI and get prescibed a course of steriods for 3 months and see if this stops the pain. If yes, then you know you have some inflammation there. Like I said, SCD does not do good at reducing inflammation in the illium, but it can help greatly to keep you in remission once the inflammation has been eliminated by using another drug like steriods. Once the inflammation is gone, a combination of the scd diet and a mild drug like pentassa could be all you need to be completely symptom free like I have been. Really, you need to see a GI to see what that pain is caused by.