Thyroid, IrregularPeriods, kidney stones

Hello Doctor, My wife is having below problems: 1. Recently diagnosed with Hypothyroidism (Lab values -> T3 = 1.28, Total T4 = 6.5, TSH = 6.01) 2. Less hemoglobin - 9.2 3. Irregular periods since last 3 months. 4. Her abdomen scan shows enlarged ovaries, with uniform cysts, probably poly-cystic ovaries. Is this PCOD ? 5. Stones in kidney and ureters. (two stones) Her urine test shows puss cells(10-15) and slightly cloudy. Urea and serum creatine are under control. we got married an year ago and are planning to have kids. Please let us know what do we need to do fix all the above problems and make my wife healthy. Also she complains that its painful during intercourse. Is it possible for her to conceive and have babies. we are worried. Please help and give advice. After doctor consultation, below are the tablets: 1. Ovabless tabs 2. Irotor-XT tabs - (for hemoglobin) 3. Urimax - 0.4 mg (for urine flow) 4. Eltroxin - 25mg (for thyroid)