Yes, brain transplants are not a viable option sadly.
Regarding stones, what about irritation from urine in the bladder back flowing to the kidneys and causing irritation? So many of us have bladder issues as well which is affected by the brain in large part or part of the down regulation you mention in Part 2.
My thoughts even prior to reading some of part 2 (still working on it) is that the body starts trying to compensate and in doing so gets further and further away from a truly balanced state.