Everything you've done sounds great. The one thing you have not addressed is increasing bile flow.
Bile flow is essential to continued peristaltic action. Bile induses peristaltic action. So you must be sure to get plenty of healthy extra virgin olive oil into your diet. Cook with it, use dressings with it, even just swallow a tablespoon of it 1-3 times a day.
it also helps to do ab exercises, and to drink a large cup of warm water in the mornings to induce a BM. colonics are great for strengthening and cleaning the colon.
But mostly, I think it's that your liver is weak and not producing enough bile. Strengthen the liver with liver-supporting herbs such as milk thistle, bupluerun, chinese gentien, dandelion, preferably in a mix of herbs such as Planetary Formula's Bupluerum Liver cleanse. You may also want to investigate www.sensiblehealth.com and see about purchasing Coptis, which encourages bile flow.
If your stools are pretty well formed, at least 1 inch in diameter, then your colon is healthy, it's just not being told to move as much as it should. :) If you are seeing tons of undigested food particles, then you need more enzymes from live foods or pancreatic enzyme supplements until your liver strengthens.