I'm going to interject a little difference of opinion here--although I do agree with much that has been posted.
I am still a newbie with chickens, and they get 'benign neglect' as management--they do what they're going to do, I hose out the 'coop' (a four-pallet enclosure with plywood over the top and plastic on two sides) about three times a year and hunt them down at night to dose with Ivermectin when my favorite hen shows up with mites. (So that's about 2-4 times a year.)
They're completely free range within my chain link fence; one wing is clipped about once a year or if anyone shows signs of taking actual flight.
I toss oyster shell on my wormbeds and they pick what they want. Eggs have only been thinshelled once, before I started giving the oyster shell as an option.
I feed a dove & quail seed mix rather than the crumbles or pellets--they simply will not eat the standard chicken feeds and waste it.
They eat a lot of the redworms in the manure under my rabbit cages; they do their official job of eating earwigs and other bugs (but won't touch a slug or snail, the chickens! Funny to watch, though...Eww, get it OFF, it's GROSS, EWWW!!!)
All in all they do pretty darn well. I let them have the occasional snack of dog food (Kirkland), which they will drive the dogs away from to get; they get occasional food scraps and when the mulberry tree fruits, they are in pure purple heaven.
So what does this have to do with you and yours? Not much.
But the best-looking and healthiest chickens and turkeys I have ever seen lived in a scrupulously-clean coop, with the translucent poly panels as the roof. It was cleaned daily per the owner, but not scrubbed. The yard was muddy but not mucky.
Some dust is normal and expectable; that's why masks were invented. Expecting chickens to live in laboratory conditions isn't practical and is rarely doable outside of a lab. I'd skip the scrubbing and organic disinfectants--let them be sometimes. Scrape/brush the perches as needed--but only as needed. Save the dusting and scrubbing for once or twice a year.
I would also recommend that you grit your teeth and euthanize your sick chooks.
It's really hard, I know--I'm rather attached to mine, too--but sometimes it is necessary to prevent their suffering and to protect the rest of the flock.
Hang in there--I'd euthanize the ones that need it, then give the coop one final scrub and disinfection with BLEACH, air it out well until it's good and dry. Then rebed and let the remaining chickens back in after treatment with Ivermectin to make sure they aren't bringing mites or worms in, and let 'em rip.
Where are you located? I'd bet we have any number of folks around here that would be happy to sell you a few extremely healthy, hardy hens.