I don't believe you are experiencing side effects due to Synthroid - I have similar symptoms and just a couple of days ago my doctor and I have discovered that my symptoms may have to do with my PARAthyroid gland. I also have Chronic Kidney disease which also has a correlation to both the Thyroid and Parathyroid.
Ask your doctor to check your Ionized Calcium, PTH (parathyroid hormone), and your Vitamin D-25 - also your cholesterol levels. Also - check out GOITROGENS - certain foods and drugs, including SOY and Milk may affect your body's absorption of your levothyroxine dose (you may not be getting enough)