Listen to your body - ANY protocol is a prototype while your body is unique... and now it is telling you what is right and wrong. Slow down on whatever causes you pain.
If your stomach is painful - this is due to the acidity of your stomach! (not the IT) You want your stomach to be acid (in order to kill the culprits: acidity in the stomach is a healthy status), this is good news... but not to the point where it is consuming itself. Any form of pain - stomach or intestinal - should have you :
1- refrain from using the trigger you've identified
2- allow for the pain to go away (and use soothing herb to help it heal)
3- reintroduce the triggers (one at a time to identify if any of these keep being the cause of the pain).
If you feel pain when using coco oil (which is soothing) you are having an important issue to address immediately.
Hope this helps,