My experience was something like yours. You are correct to make the mercury and liver connection, most do not and so have difficulty recovering. If a person has Amalgams they are likely getting mercury, if they have a strong liver, they can sustain for some time--liver will process out or store the mercury, but then stress, poor nutrition coupled with the mercury is just too much and your body starts crashing. Mercury and liver is like which came first the chicken or the egg. Did a weak liver allow the mercury to accumulate or did the mercury overload the liver? Answer is it does not matter you must deal with BOTH to be healthy. I would do a series of liver flushes, then chelation per Cutler and repeat, repeat. It can be a long process.
In answer to your original question. Mercury and liver impact many, many body systems and functions. You will be like the dog chasing his tail trying to fix each problem. Over time as you eliminate mercury and clean the liver your digestion and other body functions will improve.
PS I believe the Cutlet protocol is best and safest to deal with mercury but if you get his book he (IMO) does not adequately address the liver issue. So congrats on identifying both.