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Alright I checked her as much as I could do right now. I have some developments.If she's 4 and been in the same housing with no problem, then I would rule out ventilation.
At 4 and wheezing, I would suspect reproductive problems and maybe crop symptoms.
Check to see that her crop is emptying overnight.
I've had hens start to wheeze when they would get a bit of fluid in the abdomen due to reproductive disorders. It doesn't take much fluid to cause symptoms.
Interestingly, the symptoms can wax and wane little, at least it did in mine. Maybe their body was able to flush the fluid out, but over time it took it's tole unfortunately. Just speculation on my part.
When I got home I let them out and they ran around to the front as usual. She seemed to be doing better than yesterday when I let her out. This time I could not hear her wheezing, and she wasn't stretching out her neck. She was, however, opening her mouth when she took a breath. But that quickly subsided when she started walking normally.
When I examined her tonight, I smelled her breath, and got a better whiff this time. There was no bad odor exactly, and nothing strong or pungent. As weird as this sounds it smelled like... potato chips. More specifically, cheddar and sour cream potato chips. I could barely smell it. I... don't know if that means anything... but the info is there.
I checked her abdomen again; no noticeable change.
Now, for the black thing in her mouth. It is not a scab. In fact, it was on the other side of her mouth this time! Yesterday it was on her left, then it was on her right. Then, when I went to get my phone to attempt more pictures, I think it moved again to more towards the bottom of her mouth towards the back. I gave up on pictures and switched to videos to try to catch it, and I think it had moved back to where it was when I first looked tonight on her right side. I think I caught a glimpse of it in the videos. I'm not completely sure, it's hard to tell what is shadows and what is the black thing. Is this just something she ate moving around, or is it some kind of parasite maybe?
Whatever it is, would it be causing her wheezing?
I eventually gave up on taking the videos too. It was really stressing her out, and her breathing didn't sound very good from struggling with me. Very raspy, and rather congestion-y. But the videos did capture her breathing so I will include a YouTube link to it: https://www.youtube.com/watch?v=_spcIDutXOo
When taking the videos and examining her she did sneeze a couple times, and I have noticed a couple of sneezes since yesterday. No nasal discharge, no puffy or swollen face, and no bubbles in the eyes. Even with no other symptoms, could the wheezing+sneezing point to a respiratory infection?
Here are a couple screenshots from the videos I took. The black thing still isn't clear but I tried.

Here is something that looks like mucous. I don't know if it is actually mucous or if it is saliva.

I have 4 hens. I got 3 eggs yesterday and 3 eggs today. I don't know if she's the one not laying or if it's someone else, or if they're taking turns. Maybe I can figure that out Thursday since I'm taking off work that day.
I will check her crop in the morning.
She is still acting normal and her comb is a nice healthy red.