Well... I clean a 3x4 brooder with 14 or so chicks in it once a week. As long as the shavings are fluffy, it is fine. A bit of poo in the feeder is ok too as they will peck out the food. Water.. Good job in keeping it so clean as that is very good. However. I only deep clean the water once a week...
I personally don't keep things too clean, as the chicks do need to build up immunities to bacteria and other things they will find in their adult environment. Matter of fact. Don't feel bad to bring in a dish of soft dirt from outside and let them dust bathe in it. It will probably be better in the long run for it. Never had cocci from soil raised chicks, but did have cocci from a group of chicks raised on shavings for the first 6 weeks of their life.