Interesting. I'm having trouble with breathing as well, although it doesn't sound like it's as bad as yours yet as my oxygen levels have not been dropping below the 80's, not that this is good either.
It was picked up in a routine sleep study that was done as part of the escalation of the opiates (methadone) that I take for the pain from the myopathy, which in my case is quite extreme. My sleep was excellent, but the study picked up central apnea, where my brain was simply not sending the signal to breathe. Now it also appears to be happening to a lesser extent while I am awake as well. At first they thought it was due to the opiate, and while there is some possibility that it's making things worse, it does not match the profile of opiate induced central apnea. And unfortunately that's where I'm stuck right now, without any more answers. Mystery central apnea.
I have been experiencing increasingly troubling neurological effects and until more studies are done (awaiting CT scans since I can not be MRI'd due to metal in my body) we have no idea if it's TAM-related, apnea-related brain damage, or even psychiatric in nature (it's not as if this hasn't been stressful, although I'm generally a happy person).
So I don't have a lot to add other than to say it's interesting to see other people with tubular aggregate myopathy with breathing problems, and wanted to add myself to that list for other patients and doctors reading this. Thanks for sharing your story.