You've been killing the bugs off, have you flushed the junk out of your liver?
When the colon is clean, the digestion should start to right itself even if it does take a while.
I did the LBB from Barefoot for about a year, then did the Schulze colon cleanse with the #2 formula that got the junk off the colon walls. There was a lot of colon junk that made food go thru me like this, too. Colon needs cleaning, but if you've killed the parasites off for this long and haven't flushed the liver, then I think the liver needs flushing soon.
I'm not Doc, but I've worked this program for over 2 years now. So this is my experience.