Thanks for using the forum. I am happy to address your questions, and my answer will be based on the information you provided here. Please make sure you recognize that this forum is for educational purposes only, and it does not substitute for a formal office visit with a doctor.
Without the ability to examine and obtain a history, I can not tell you what the exact cause of the symptoms is. However I will try to provide you with some useful information.
Muscle cramps are not an uncommon manifestation of a systemic viral illness or other infectious etiology. Muscle cramps may be due to myopathy. A myopathy is basically a generic term for a muscle problem. Myopathies can be inflammatory, as is the case with a disorder called polymyositis which is an autoimmune disorder. Also, there are genetic myopathies, of which there are several, each with its own characteristics and features. Finally, and probably most commonly, metabolic causes such as thyroid problems or low potassium can be the cause of muscle cramping. The latter two can be diagnosed with simple blood tests.
EMG in addition to simple blood tests such as a CK level can assess for the presence of myopathy, and can also diagnose/exclude ALS. I am not sure if you need a muscle biopsy without further noninvasive testing and results.
Certain medications, particularly cholesterol medications called statins, can cause muscle cramping. Also, ciprofloxacin is known to cause tendon inflammation. Azithromycin and doxycycline do not typically cause myalgias but rarely can cause sensory abnormalities.
Lastly, fibromyalagia is a medical condition that leads to whole body pains. Its cause is unknown, but it is characterized by diffuse aches, sometimes GI symptoms similar to irritable bowel, sleep abnormalities, low pain threshold, and other features. It is best treated with medications such as lyrica and neurontin, exercise, and physical therapy.
Do you have a neurologist you follow up with? If not, you may benefit from having a thorough evaluation and review of your history. He/she may recommend further testing (such as lumbar puncture, muscle biopsy, repeat MRI, etc) based on their findings.
Thank you for this opportunity to answer your questions, I hope you find the information I have provided useful, good luck.
Sounds like your syptoms are the same as mine. The only antibiotic I took was cipro and I'm sure without doubt that this is the problem. I can't offer you much help as I'm still pretty bad myself. Check out fluroquinlone toxicity on Facebook you will get some facts and advice on there