As for the cause god knows. Could be fungus,parasites,virus,bacteria,stress, ect ect
Fixing it you have to see what food cause a reaction. Your best bet would be to got on a fruit only diet for a few weeks. If your systoms improve your joint pain will be the first one to improve if it is leaky gut.
Then really just stick to the fruit diet and let your gut heal. It doesn't sound like fungus and even if it is a fruit diet will not feed it because you will not be eating fat. It's fat that spikes your blood Sugar levels and that feeds the fungus.
Easyest way to do is stay on a banana only diet. Your a women so 20 RIPE bananas a day will do the trick that equals 2000 calories.
A ripe banAna has tiny spots on it or big round spots.
Diet plays a huge role in auto immune and leaky gut.
What's happening is food protiens are passig through that gut wall and into the bloodstream large ones that shouldn't be.
This makes the immune system go crazy and it starts attacking your body. It is extremely serious and deadly don't mess around with it.