It sounds like you are experiencing die-off symptoms from the diet. What could be making it worse is that your diet feeds the bad bacteria in the gut, possibly perpetuating the die-off. Have you done any candida tests? Your diet is not good enough to kill off the yeast and thus are making you feel bad.
The acid reflux symptom is likely due to lack of stomach acids, namely HCL (hydro chloric acid). If you supplement yourself with HCL you likely will notice an improvement.
If you are not protecting the liver, this is the main organ that makes you feel bad with malaise like feelings.
Western medicine doesn’t cure things in my opinion, but only treats the symptoms.
Hope this helps.