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It makes more sense to me to aim for exercise that uses a little of one muscle, and then a little of another, so as not to sustain the stress on any one muscle
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perfectly correct. This type of exercise may or may not improve your muscle strength (depending on the severity of your illness and how much stress your muscles can sustain), but not less important it will help you learn how to plan your movements so that you can do what you want much better.
It may be a good idea also to work with someone and not do it on your own.
I had an excellent teacher. for more then a year, in twice weekly sessions, we meticulously learned each and every one of my muscle groups. (she used a system called movement notations, which was originally structured for choreography, but is excellent to document any type of movement).
I learned to use my muscles in such a way, that I had significant improvement in my functional level, despite gradual worsening of my illness.
(that I stupidly ignored, being reassured by my neurologist at that time, despite the concerns of my pulmonologist, but that's another story).