Shalynn, I know, I sometimes really can't understand why people look but don't respond. I wouldn't take it personally, though, some people really are not feeling so hot but still like to read up on everyone anyway. I'm actually in that category right now. I have way too much going on but had to make some posts - I hate it when people are sick and feel all alone.
I'm so sorry you saw a generalist at Mayo. It would've been very helpful to have seen a specialist. No, muscle atrophy isn't necessarily specific to one disease but a smart neuro could put all of the clinical and testing evidence together! And if you have a mitochondrial problem, will they then have to do yet another biopsy? They are not fun to endure!
Don't underestimate the helpful nature of sublingual B12. I've read any study I could get my hands on, even books from the early 1900's. It takes time to heal but it really does help. I had a severe B12 deficiency back in 1997 - 99. The shots did not help to heal my peripheral neuropathy, only the sublingual did.
If you end up having a mitochondrial issue, CoQ10 has been proven to help. I don't have time today to get you a site but you can look that up in PubMed.
Please do get copies of ALL your test results. You'd be amazed at how much doctors don't tell you. And B12, for use as an example, can be 400 or less and you can have nerve damage. My homocysteine was high during my B12 def. and they often test that and methylmalonic acid too.
And I have to say that you can have a copper deficiency and still have a neuromuscular disorder!

I think doctors sometimes forget that patients can actually have more than one thing wrong with them.
I think it sounds like your doctors are headed in the right direction. Most doctors don't know about CMS and it isn't even a thought in their head. So you may have to bring it up. Here's the best site for that.
http://neuromuscular.wustl.edu/synmg.html
Good luck! Please keep in touch. It's just a little slow right now. People here are really nice and are great at giving good advice and support.
Annie