I 100% agree about liver issues of ANY kind causing hormonal changes - I have been victim to that myself. I also hear quite often of the connection between parasites/bacteria and gallstones.
My advice would be to take the following four supplements to gradually eat away at stones (in order of importance) - Malic acid, choline (ideally with inositol, you can get these 2 in a single tablet), sulphur (garlic, MSM, onions, radishes) and either GCG or Chanca Piedra. This should be enough to nuke stones cold lol, if done at the same time as flushes I think it will really help :)