These flakes sounds pretty much like the candida specks.. if so they are candida "eggs". THe way it reproduces (seeing them is a good sign).
Excruciating pain means- you are doing something utterly wrong.
There are very FEW pain centers in your intestinal walls, if you feel pain SLOW DOWN on the Candigone or whaterver you have started that might cause that pain= go for a raw veggy only diet until the pain is gone.