Let's look at a few things - compare to the last time you had chicks.
Your eyes are watering. You have a new brooder - what's it made of?
Did you use newspaper last time or something like puppy pads?
Homemade cleaner? What are you using, have you used that before?
Feed - using the same brand as before?
Heat lamp - same bulb as before?
The mention of ammonia was not the cleaner, it was that poop gives off ammonia which can be an irritation to the nose/eyes and is offensive.
Personally, I don't use newspaper in an inside brooder. Puppy pads work better, they are more absorbent and seem to keep odors down. I change out puppy pads daily in the first day or two, then may need to change certain areas out 2-3 times a day depending on "poop load"

Again, personally, I don't clean the brooder with anything. Changing out pads and bedding is all I do. I keep water station(s) and feed dishes cleaned daily.
Some feeds can have a smell especially when wet. Is there any wet areas where feed may have gotten wet, water station leaked and wet the wood, etc.?
The wood you are using - what type is it? Pine, cedar, etc. treated or untreated? Certain woods can give off some odor especially if heated (like under a lamp) or when wet.
Most of the time I try to get chicks outdoors within the first week or so after hatch. The bigger they are the more they eat, the more they poop and the more they get stinky.