Well, you're probably right and the CD could have been around longer than your diagnosis. I suspect that was the case for me too. I hope the Jpouch will work out and you'll have a life-long remission.
When you were on SCD, did you find it improved your symptoms? Even if didn't help the CD much, it might be worth it just to have relief from the symptoms. You can always modify your diet to suit your needs too. Just a thought.
I think I noticed a much bigger improvement from having a sugar free diet and only drinking water.