liver pain: no disease. congestion?

New to curezone here and looking for advice and help on an ongoing problem i've had where my liver is located. here's a little bit of history: beginning a year ago had a very stressful time with little sleep, began having Sugar cravings, weight gain, Depression and anxiety, stopped menstruating (havent since june 2014), and had reflux of my food with gnawing hunger pains after eating. i had high bilirubin in my blood beginning in may, high eosinophils (indicative of bacteria/parasites/ food allergy ),excess bile in my stomach evident through an endoscopy in june, diagnosed with lymes disease in june, went on Antibiotics for it, an ultrasound in july showed a slightly enlarged liver, got ibs symptoms in july, began having episodes of severe fatigue and Depression and anxiety. i was diagnosed with hashimotos thyroiditis (the autoimmune disease that attacks your thyroid) in august. went on thyroid support medication and immediately got worse, so fatigued that i could barely do anything, having extremely dark/reddish circles all around my eyes, skin turned a yellowish color but not eyes, and severe pains on the right lower rib/liver area, with nausea, muscle twitching, and blood in my stools. blood tests showed elevated liver enzymes (ALT and AST, direct bilirubin, indirect bilirubin, total bilirubin). tested negative for liver disease, MRI was normal.
the doctor said its just gilberts disease but i dont believe that because the pain in my liver area and the fatigue and dark circles are so bad that just bending down hurts my side. i have a colonoscopy for next week to see if it is my colon that is the problem.
my thoughts are...can liver congestion cause pain?
can Gallstones be present but not picked up in an MRI?
can liver congestion be related to why i dont menstruate?
im waiting to hear back about whether or not i have adrenal fatigue. can adrenal fatigue cause liver pain?
also, i follow a paleo-autoimmune diet so i have removed food allergens.
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