Your symptoms sound familiar to me. I have Lems and the muscle aches are a big part of my problems along with the MG like symptoms. I tested negative for Lems the first time, but when I was in the ICU they tested me again for Lems and it was positive. I also respond well to mestinon, which confused doctors because I also had only mildly abnormal EMG.
I blamed a lot of my symptoms on thyroid, because I also had a total thyroidectomy in 2008. My thyroid levels have been either hypo or hyper, but they definitely affect whatever myasthenia you may have. I find that Armour natural thyroid works 1000% better for me. Synthroid makes the TSH come into normal range, but free T3 levels are still low, so I feel lousy.
Hope you can get things figured out.