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They are closer to the floor than you, so it will affect them more. From what you describe it sounds like it really could be the new shavings that caused the congestion....I had similar symptoms in some chicks when I added a bit of fresh cedar shavings to a flock lounge area. The lung irritation might take a little time to go away even after you remove the shavings, so you may hear that wheezing for a couple of weeks after they are no longer on the shavings.
I recommend people getting down on their hands and knees to determine air quality - where the chicken lives.
Nipple waterers are great for keeping the water clean....wonderful for meaties! The nipples are easy to obtain and install and you can use just about any kind of container to make a nipple bucket...
The commercial industry uses nipples from the get go. It's the way to go. I like drinker cups for older birds.
I hate winter with chickens cause I have to shut down my nipple/drinker system.
Next year I'll have a circulating warm water system for the nipples. I'll love winter again.
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Mentioned about this above. The shavings are great...just got to know how to work around them. Elevating feed and water out of the litter makes things easy...using nipple buckets make it the easiest of all.
I put feeders and waterers on bricks and keep raising them to keep the brims at birds back height.
When using the big flake shavings I didn't notice any of my meaties eating the shavings, even those with food on them. I just let them eat around the shavings that happen to get into the feed and would even knock out old feed right into the litter for them to clean up. No worries!
The feed store by me sells inexpensive large bales of horse stall pine shavings and that's what I use. Probably what you're using.
Like Aoxa, mine were done with a heat lamp at 3 wks and out on range at 2.5 wks at temps cooler than those shown here. I'd start weaning them off that heat lamp by only using it at night and raising it higher and higher each night until they harden off and grow out feathers.
I have one or two warm spots and lots of cool space for brooding. The chicks tend to wean themselves.