Sorry you are feeling so rough
It could be a combination of things.
Dr Wallace ( very high profile US lupologist) says that 5%-10% of patients suffer musculoskeletal flulike symptoms of aching and fatigue but the symptoms resolve within one to two weeks even if the therapy is continued.
I think it is very unlikely that Plaquenil would be affecting your muscles in a clinically unacceptable way after only 11 days. It is a very rare side effect anyway. Although people occasionally report benefits after a few days only this is most likely psychological
Another possibility is emotional and nervous reaction to finally getting a diagnosis, when the sense of achievement and validation masks a whole range of other emotions for while. It can take a long time to fully realise the implications of a chronic disease and people tend to think all their problems will be solved when they start on medicine.
It can take a long time too to find which medicines work best for each person.
Another possibility might be that the gastrointestinal effects have been severe enough to cause problems with electrolytes, dehydration.
I agree you should put in a call your to doctor although that could be quite hard to do.
Personally, I would stop taking it for a couple of days to give yourself a chance to recover and then start again slowly. I think you are only 200 mgs a day you could try taking it every other day. It takes weeks to build up in the system.
I know too that you have a very demanding work load so one way and the other you are under even greater stress than usual. A few quiet days at home would probably do you the world of good if at all possible. Rest is so important physically and emotionally.