In the beginning I too noticed strange moving around of aches that would start and stop. Mostly for me it was the upper or lower part of my body would not feel good at the same time. My chiropractor was always puzzled as to why this was happening. Back then I didn't really understand it so I was no help to her understanding it. Like you said...the pain would suddenly just stop in a certain area that you constantly had trouble with but a new area may start aching for no reason.
Without faith, I would have never stuck it out long enough because I would have just assumed I was doing something wrong. I just kept visualizing my body having to process all thoses NPN acids little by little, layer upon layer. That is why we are to go slowly in the beginning.
In my opinion, the full body baths help the most for a person in your condition (my condition) and I'm just going to say this as my own opinion and not ML's, but you might try using magnesium oil or make your own lotion using dissolved epsom salt in a very natural base lotion to rub all over. The magnesium oil stings in the beginning a little but the skin will absorb it and the stinging usually stops after a while. That it the only idea I can come up with for someone who can not take the baths or up their oral intake of ES.