First of all

to you while you are working through hospital issues with your parents. Hang in there!
Am I being controling for putting my foot down and saying I am not going apologize for having my period as I have to every month to him?
Yes I am...
and that's a good thing! What I read above is about your body and your health and
inside your boundaries, therefor you SHOULD be controlling of that. Unapologetically.
Controling for standing up to him and saying I won't be in the same bed with him while he is contagious? I have an autoimmune disease
Again, yes you are being controlling ...
and properly so. Your health, your disease, your sleep. You set the ground rules (with appropriate medical advice) regarding your health.
You do not get to control if others accept and follow those rules. That's inside their boundaries.
Therefore it's proper that you make the decision to not sleep in same bed with him.
Meanwhile there's a physically healthy man at home who refuses to do even the simplest thing that others do every single day.
Perdita I would resist making judgments for which you lack qualifications. Only doctors with all the facts can determine the status of his physical and/or mental health.
My understanding is you are not going to "force" the issue on health, therefore we simply don't know.
You can't control his doctor decisions (outside your boundaries), however you can control the "type" of person you live with (especially due to your health status). That's inside your boundaries.
It also speaks volumes about his care for you that he exposes your poor health to his poor hygiene.
Also raises the question about why you continue to expose your poor health to the possibility of compromise by being in a home with him (even if you do use different bathroom and bed).
Seems risky to me.
I am tired in every way. When I was single for nearly 20 years I had to do things alone. Now, instead of having a man that is a team mate to me, I find myself having to do things constantly for him too.
No
Perdita you don't
have to. He doesn't have the power to force you.
For some reason you are choosing to do these things. I would suggest that's a place to reflect on for a while.
Best,
FF