What kind of bowel cleasing are you doing? you really need to flush out everything that was put there by the LF.
Sadly, a stronger liver means a liver that will detox faster, it will go in cycles, it will get better, then get worse, and get better again -- you can avoid it to some extent via colonics. What is your diet like? your stronger liver may react to certain things, things that it ignored before.
The liver IS the organ that must be cleansed, if you got out stones then you for sure know that your liver is heavily congested, not just because of stones, but you need lots of bile for good digestion, the liver also detoxes itself via bile, the less bile that can be released, the less toxins it can draw out from the blood, the body generates daily toxins as normal and you need to deal with this AND whatever else ontop.
Anything created by the body that isn't dealt with by the liver, just becomes toxic waste after a while.