I had problems with the intro diet, too. Not sure what the culprit was, but ima's right: some foods that are "SCD legal" may still be a problem for YOU.
My advice would be to move on to SCD legal foods that you feel intuitively are safe for you. Assemble a small group of these foods and try to stick to them for a few days. If things smooth out, you'll know you're on the right track. Then you can add new foods in, one at a time, and see how you react. Keep a food journal to track symptoms.
In my experience, the principles of the SCD are sound, but the stringent rules and guidelines can be detrimental. I don't believe there's a one size fits all. The 30 day rule isn't accurate, IMHO. I struggled with the SCD and even had the author tell me to give it up, but I was determined. I found there were foods that I'd probably never tolerate - the yogurt, for example - and there were some foods I couldn't eat early on that don't bother me now - like nuts and raw veggies. It's up to you to tailor it to fit your body. That requires a lot of trial and error, which can be frustrating. There is no shortcut and, ultimately, no one can tell you the diet that will work for you.
In addition, I'd also add I feel dietary changes are only one part of the healing equation. You must also rebalance your gut ecology - get rid of or reduce bad gut flora and reintroduce the good - via probiotic supplementation. I also found there were several natural supplements that helped heal the gut and reduce inflammation.
One final note: These things can all work in conjunction with medications. It doesn't have to be all or nothing. Even though I've been in remission for a long time, I still take a maintenance dose of sulfasalazine.