Nicholas, your questions are big ones - and deep ones. Most of us here are not medical or therapeutic professionals, but I can say one thing, which isn't going to help you in any specific way - and that is to tell you that without a doubt, our minds and our bodies are inextricably connected.
There is probably no one answer for everyone, because everyone's early childhood experiences are all so different. Anyone who suffered from abuse or neglect of some sort during childhood will have emotional and mental and therefore also physical problems.
There are some mental diseases which clearly have a genetic component. But they will be made worse in the child if the parent suffers from the same disease without treatment, and inflicts their own illness upon the child. I got to know a girl in foster care who suffered from intellectual brain damage due to her mother's alcohol consumption during pregnancy. But the mother suffered from the same brain damage due to HER mother's drinking - and the whole family had bi-polar disorder, which is why the mother and the grandmother both drank. The girl I knew started taking modern medication in her teens and did not become an alcoholic (she is now approaching 40) but she was always physically frail with many complaints. Her two children do not have the alcohol brain damage - but because she does not function normally, either intellectually or emotionally, her children are emotionally damaged due to her brain damage and bipolar disorder. As they approach their teen years, the chances that one or both will have the bipolar themselves is very high, but they have both shown many signs of physical TMS symptoms, along with anxiety, most of their young lives. It's absolutely tragic.
Having said all this, I guess I can tell you one thing definitively - which is that the physical symptoms that we label TMS, are not distinct from, and can not be treated separately from, a person's mental and emotional disorders.