C.M.
Some thoughts that spring to mind:
1) Are you watering down his juice? Kids shouldn't have more than 8 ounces of juice a day total, and it causes fewer gastric issues when cut in half with water (also makes them think they're getting more!);
2) Cow milk allergy/intolerance - you might try switching to goat milk for a couple of weeks. It is vitamin D fortified like cow milk, but does not have some of the proteins that cause reactions in some children. My kids are allergic to cow milk (hoping they outgrow it!) and are doing very well with the goat milk. Also has the bonus of being antibiotic and hormone free.;
3) Less fruit and more veggies - kids tend to prefer fruits because of the sugars, and a good way to tell when they are eating too much of a good thing is the big, soft poop. It can inhibit the body's ability to absorb iron, so something to consider.;
4) Have him tested for celiac - better safe than sorry, since this is one of the signs.;
5) Try switching to Pampers Cruisers (and maybe going up one size). We found the cruisers seem to work better with boys.
Good luck! You sound like a great mommy.