If rotating the foods seems to help maybe it is best to keep doing so. I did the food rotation earlier on this year because I read that it would be helpful in terms of healing my leaky gut. I noticed that while doing the food rotation I was able to tolerate more foods. Whereas if I eat the same stuff everyday, sooner or later, I will react to it, no matter what it is ( and this also includes allowed foods on the forum list such as eggs!). I have no idea why the food rotation works better. I am only guessing that there might be some kind of accumulative effect, maybe due to poor/slow digestion and slow transit time (?).
Another issue is that if the transit time is slow (if he is already constipated and the food stays in too long), some foods that are not so easily digested may not be completely digested and then start to ferment in the gut causing all sorts of problems. Grains, especially glutenous grains, can be hard to digest for those whose digestion isn’t working optimally. Another problem with grains may be the fiber; for someone who is severely constipated already fiber can only agravate the problem. I know people say to eat fiber for constipation but for me this only made things worse. What helped me was adding more fat to the diet and starting the day with vegetable juices (to which I added raw egg and home made sour cream for the fat).This is something I picked up from reading about the GAPs diet which you might be familiar with if you’ve been on Autism forums.
Try some of the non-gluten grains like buckwheat or teff. They may be easier on his digestion and they are tasty. I order my teff from iHerb and use it to make breads and pancakes. I seem to tolerate both just fine.