Hi
Welcome to the MedHelp forum!
Unexplained aches and pains coming on and off could be due to fibromyalgia, chronic fatigue syndrome, rheumatoid arthritis, lupus, Crohn’s disease, H pylori infection, anemia, liver disorders, diabetes, hypothyroidism, Vit B12 or Vit D deficiency and due to calcium or magnesium deficiency. It can also be due to sleep related disorders. In women it can be due to hormonal disturbances related to PCOD.
Since you also have diarrhea and constipation, Lupus and Crohn's should be ruled out first.
Please consult your PCP for primary examination followed by proper referral.
Take care!