The model that I am assuming for conditions like CFS, is some event triggers a microbiome shift which persists in a dysfunctional state. A few of these events are well known, or suspected:
- Infection (viral or bacteria) – best documented example is Bergen Norway – giardiasis
- Vaccinations – in theory should, no studies done on microbiome shifts before and after vaccination (yet!). If the vaccination works, it has been shown that depends on the microbiome being right 
- Antibiotics or antivirals
In reviewing a news article, The fascinating effect a stroke has on the gut microbiome, reporting on the International Stroke Conference,
Prior research from the same team revealed a stroke does have an immediate effect on the microbiome, but how long these effects last for was not known. Using animal models the researchers conducted microbiome examinations three days, two weeks and four weeks following an induced stroke…. A notable decrease was seen in Bifidobacteriaceae, a common bacteria found in probiotics, up to four weeks past the stroke, while increases were seen in Helicobacteraceae across the same observational period.
Another intriguing change in the gut seemingly brought on by the stroke were notable abnormalities in intestinal tissue. Normally in healthy animal models this tissue appears structured in orderly ways, almost like branches of coral. However, close examination up to four weeks post-stroke revealed the villi, structures that project off the intestinal wall, were scrambled and visibly quite different from the healthy models.The fascinating effect a stroke has on the gut microbiome,
The real interesting aspect of the article was:
Another compelling study from 2017 suggested magnetic simulation to specific areas in the brain can affect the composition of a person’s gut microbiome.The fascinating effect a stroke has on the gut microbiome,
The question is then — do cell phones create magnetic fields (that could potentially stimulate the brain). The answer is yes:
Among the valves tested, the settings of the Strata valve, the Hakim valve, and the Sophy valve were affected by magnetic flux densities of 6.0, 17.5, and, 40.0 mT, respectively. Cell phones produce a magnetic flux density of 3.0 to 40.0 mT.Effect of cell phone magnetic fields on adjustable cerebrospinal fluid shunt valves 
And for Wifi, the evidence is cleaner still:
The pure cultures of Listeria monocytogenes and Escherichia coli were exposed to RF-EMFs generated either by a GSM 900 MHz mobile phone simulator and a common 2.4 GHz Wi-Fi router. It is also shown that exposure to RF-EMFs within a narrow level of irradiation (an exposure window) makes microorganisms resistant to antibiotics.Evaluation of the Effect of Radiofrequency Radiation Emitted From Wi-Fi Router and Mobile Phone Simulator on the Antibacterial Susceptibility of Pathogenic Bacteria Listeria monocytogenes and Escherichia coli. 
While we know that all of the above can cause microbiome shifts, most people microbiome returns to normal. Most people. As a statistician, I know that as the number of low risk events increases, the chance of a significant event cumulates.
We cannot say: Wifi, vaccination etc causes any specific long term autoimmune conditions, it just increases the risk — like smoking does. There are people who seem immune to the effects of smoking (like the Comedian George Burns who lived to 100 and love smoking cigars).