The paper about blood transfusions says: "As viruses and possibly other micro-organisms seem to be able to trigger an acute onset of CFS". That's 'trigger', not 'cause'. It doesn't mean that the ME state is maintained by a pathogen, or that removing the pathogen would remove the ME state. Pathogens may trigger ME, and ongoing infections can worsen some ME symptoms, but nothing shows that they are part of the core dysfunction that is ME.
An increased prevalence in families shows a link, but doesn't indicate that a common pathogen is involved. Likewise for outbreaks: a pathogen might have been the common trigger, but maybe some pathogens are more effective at triggering ME than others, or there might have been some environmental factor that made the victims more susceptible to triggering.
The doctor who believes that ME is due to a bacteria in the kidneys should inject a sample of the bacteria into rat (or other appropriate lab animal) kidneys and see if they develop the ME state.