Simply sounds like you have dysbiosis in the early stages. I didnt have stomach problems until late in the disease myself. It actually doesnt start off as a stomach issue. Acne medications like tetracycline/doxycyclines cause candida/bacteria overgrowths.
Having faint fungal infections on feet, genitals, mouth, fingers hints to a candida issue. You also could have some heavy metal issues too since the good bacteria helps rid of heavy metals we get from food and the environment ect
solution: Flood your body with probiotics like VSL 3 DS to see if you fungal infection goes away. It should start to subside...