@bohemian - I'm sure you know kidney pain can be caused by a kidney infection and kidney stones so those should be ruled out.
Having said that, I've had pain in my right kidney for over 30 years. I had an ivp done way back when, it showed nothing wrong, and that was all the doctor did.
In the intervening years I switched to filtered water and quit smoking, both of which helped the pain (but it didn't go away completely). For the last several years I've been taking cranberry softgels daily and they seem to have stopped the frequent UTI's I was getting.
When I was pregnant with twins in my early 20's I had a severe kidney infection, and I've often wondered if it caused some sort of damage to my kidney.
Anyways, this may not answer your question at all, but maybe it will help you a little - I'm guessing my kidney pain (which is now so slight I have to concentrate to feel it) is probably not related to CFS/ME - it started years before I developed CFS/ME.