Only other suggestions: Feed' them nothing but the layer pellets and only clean water (no ACV) for time being. If they don't have a bowl of grit available, get some. I'm going to assume same feed/feed manufacturer. Just minimize range of variables.
When you ID the source(s) of alteration in quality, please post up findings. Best of luck on the investigation, and congrats on your `olfactory sensitivity'
Oh, forgot on the raising of coop off of ground: We used some old, treated 6"x6"s that we had left over from another project (also, wanted to make sure County Assessor wouldn't nick us on taxes for `permanent' outbuildings - both coop and shed can be `levered' along the `runners' to another location if need be). Check the coops sub-forum as there are plenty of examples of a multitude of ways to `elevate' coop.