My daughter is only 22 months, but has similar abdominal issues, also mostly at night. We have been to a number of specialists, had several tests done, and tried dietary restrictions for my daughter and still don't have answers ourselves. I strongly concur with those who have mentioned seeing a naturopath, and suggest that you don't give up seeking answers.
However, we have found something that works wonders in the meantime. A friend suggested we try a particular blend of essential oils called Digest Zen. I put several drops on her tummy at bedtime. When she has it, she sleeps well. When she doesn't, she is sobbing in pain within three hours. Because of this and an experience with my epileptic husband, I am now a distributer for the company that provides the oils. Please let me know if you'd like more information. (____@____.com)