First of all, keep in mind that I am unable to diagnose you because I am unable to examine you, this forum is for educational purposes.
From the story you present I suspect this is just a fraction of your medical history and there is much data that I do not have. Many of the signs and symptoms you describe are compatable with a mitochondrial myopathy such as MELAS, MERFF, etc. These mitochondrial disorders can be associated muscle fatigue, peripheral neuropathies (tingling of the feet/toes), seizures, migraine headaches and stroke-like episodes.
I would recommend that you see a metabolic/genetic neurologist (in major academic centers only) to test you for the common mitochondrial genetic defects, assess your serum/urine amino acids, urine organic acids and a MRI of your brain. An EMG to evaluate your tingling feet would also be helpful. Pain is common in all myopathies, but stiffness is non-specific and can be related to your muscles, a brain process causing spasticity, or joint disease. Treatment for mitochrondrial myopathies is limited at this time to vitamins to enhance mitochondrial funtion including Co Q10, B-vitamins, and carnitine. Mitochondrial disorders are a multi-system disorders (brain, heart, neuro-muscular, internal medicine etc) and require a team approach.
As far as your ANA is concerned, the speckled pattern is non-specific and is seen in many disorders including SLE, scleroderma, mixed connective tissue disorder, thyroiditis, etc. A 1:640 is a high titer and is concerning. I would definitely see your rheumatologist again and have your ANA rechecked, (if due to your thyroid, it may be a lower titer now). You should also have a SSA/SSB, etc panel run (probably already done once by your rheumatologist). A paraneoplastic panel may also be useful. If you continue having joint pain, maybe a joint aspiration with help determine if this is an inflammatory condition.
I hope this has been helpful.
Few comments
1- the muscle biopsy is a gold standard for the diagnosis in your case , as few other things aprat of mitochodrial dysfunction could cause a proximal myopathy and respiratory muscle weakness with more frequent myalgia
2-Myalgia is generally a rare symptom in myopathy and suggests orthopedic and rheumatic causes especially if noprmal CK!
3- CK could falsely be normal in case of end stage myopathy with atrophied muscles or if using steroids or if the cause is hyperthyroidism
In brief, yes you should see a rheumatologist again
Bob