One more thing (as if I haven't said enough already!) - it sounds like a lot of things "cascaded" with your dad. With CIPD, it appears that sudden pain in the back isn't all that uncommon. Since he has both CIPD and MG, he is much weaker than most patients usually are. Chances are that lying in bed for a while with a hurt back and weakened muscles brought on the pneumonia (he wouldn't have felt like coughing up any mucus that accumulated, which would have likely caused it to get infected).

Once he developed full-blown pneumonia, his muscles were weakened even more (and I'm sure that his back hurt more, too!), which meant that he couldn't get rid of the infected mucus, due to his inability to cough. My bet is that while he is weak as a kitten right now, if he is able to stay on strong antibiotics and he keeps taking his meds he will get better with time, lots of rest, and plenty of TLC. Just be sure that the head of his bed is elevated enough that the mucus doesn't have a chance to sit there and cause more problems.

In addition to a PT, do they have a respiratory therapist monitoring him? He will probably not be able to do as much as the RT would like, but they can keep tabs on him to see if he is getting better or to let the doctor know if there is cause for concern.

Are the doctors continuing him on medication for the MG? It's possible that they may be so concerned with treating his other symptoms that they forgot to include the MG meds as part of his regimen.

If he doesn't have one already, you might want to ask the doctor about the possibility of getting him an adjustable bed - like a hospital bed - to sleep in at home. That way, he can sleep slightly elevated if he needs to in the future. Most insurance will cover the cost of a bed if it is determined to be medically necessary.