I would address your drainage problem first. I've used deep litter for many yrs, barely ever clean the coop, no poop piles, no smell, everything breaks right down to powder, great stuff to mix in the garden. I always use sawdust and dry tree leaves for bedding, both free. I shy away from hay or dry grass, those can mold.
Moisture/poor drainage in the run, not much of a issue other than it would be better dry, there is unlimited ventilation in the run. In the coop though high moisture will give you problems, poo won't break down, ammonia, etc. Having good ventilation in the coop is very important also, especially in freezing temps, moisture breeds frostbite. Mine only has ventilation through the open rafters, 8' roof so no breeze on chickens. Pop door is always open also unless we are getting subzero weather with -20 windchill. Very little frostbite at those temps, none on hens, only the tips of the combs on roosters (no loss of tips, heals in the spring).
If proper drainage can't be obtained a raised floor is a option. My father raised chickens for many yrs in a 20'x20' log cabin style coop with a raised plywood floor using deep litter. He had many chickens in it for around thirty yrs, floor is still solid today, well ventilated dry coop. Coop sits on piers so not enclosed underneath, well ventilated.
As far as medicated/ and or fermented feed, like someone else said "It's about your comfort level with risk". Not against using medicated, I just never have, and chick losses have always been minimal, and some batches zero losses.
Just how I do it. I feed fermented mash to all my chickens, but chicks get just starter grower dry. As soon as they get a little bigger, feathering out I feed them it wet, one so they make less of a mess in the brooder, two so the eventual transition to fermented is less of a shock.
I've heard cider vinegar with the mother is good for chickens, good for us, I've just never used it. I caution against using it to ferment your feed, I say this cause some do, fermented feed is supposed to be a lactic acid ferment, just like sauerkraut or kimchi, and will have the same beneficial bacteria as yogurt. Adding cider vinegar makes it go acetic acid ferment. The enzymes in cider vinegar are PREbiotics and not PRObiotics. They can actually prevent the growth of good probiotics when put into the wet feed, and can even make it go alcohol fermentation.