I believe that Liver Flush will not be affected by gut flora imbalance. The best way to solve all your problems is to start with your stomach. If you do not have enough acid in your stomach to begin with all your problems will continue. You can do the baking soda acid test. You can find the protocol on CZ by searching. Secondly, you should definitely take probiotics, Kefir and regular yogurt are great, you are on a good path there. If you can make yogurt at home from organic milk that will be better.
Liver Flushing will be helpful in building good flora. So continue doing so.
Are you curbing your fat intake for at least a week before your flush? Try eating raw vegetables only for a week and then do the flush. I fast one day before my flush.
Have you tried coffee enema, that also will help with liver cleanse and gut flora.
Do you eat cayenne pepper? It has lot of benefits, including cleaning liver and your arteries, among others.