Try a digestive enzyme supplement...
Not Cathe, but here's what works for me... I had the same problem until I read something Tosca Reno (a clean eating guru--if you don't already know who she is) suggested. I take a digestive enzyme complex before each meal. The one I take I get from Sprouts (which is a health food grocery store around here). Basically, you want to look for one with Amylase, Lipase AN, Protease 4.5, and Bromelain. Those should help with the high amount of protein and fiber you eat on a clean-eating program. I can definitely tell a difference when I forget to take my enzymes before a meal--especially a meal with a high amount of protein and fiber. I feel really bloated. Drinking lots of water helps, but if you've got a sensitive stomach, like I do, it won't eliminate the problem completely. It may just be worth a try for you.