Ok this may get complicated, and it's new (and very exciting) information that might applly to your kiddo here.
First, I highly suspect some sort of air sac infection (airsaculitis). There are many kinds, many causes, some scary, others not so. It seems when i was doing research, all I find are the scary MG related ones. There is no indication that this bird has MG and, given his absolutely sad state of health (which you're kindly repairing) if he did, he'd just flat die. So I'm ignoring MG related airsaculitis as a backburner item now and suggest that you backburner-it too.
Not that we should forget it - but there are other things that seem quite more likely.
Here's the weird part, and I should know this as my bird is experiencing it right now.
If there is a (get this) broken bone, particularly the humerus, the air can inflate the adjacent air sacs causing inflation. In the case of my bird (who had an amputation causing a forced cut of the bone which is leaking air into the adjacent tissue) this is supposed to cease over a week and deflate. Thankfully it's happening earlier.
Flock history: you initially suspected this baby as having a fracture. But I don't recall that it was the humerus. If you look at this skeleton, which bone did you suspect he broke:
http://www.krassesrudel.at/forumbilder/thecoop/figure3.gif
I just thought it an *extremely* odd coincidence that broken bones were brought up.
Now, in practical reality, one of the causes of airsaculitis is E. coli. E. coli is a coliform bacteria, present in all healthy birds in small amounts, but can be spread through feces, bad environmental conditions, and blooms in birds with depressed immune systems and bad caretaking. If any bird had those conditions, this little guy did! E. coli invasion of the air sacs sometimes result in a yellowed exudate within the air sacs. Do you see anything like this? (Of course that's probably observed through necropsy and we don't want to see a necropsy of this baby for another 10 years!)
Another issue, which wouldn't surprise me, is that aspergillosis also can cause this. Aspergillosis is a fungal issue, and often results in poor environments. Again - fits the bird. Though I think it's usually associated more with nodules in the lungs than the clavicular air sacs I believe you're seeing.
The problem is that if this is airsacculitis, it could have come from the bone and spread to the air sacs, or it could originate in the air sacs and possibly infect bone. I think he has other more pressing issues, but it would be nice to treat this.
Can you tell me whether this is new - this pair of airsacs, or do you think they've been like this the whole time you've had him?
The other issue is that to treat, what do we treat? We don't know the true causative agent. Aspergillosis is fungal and requires one type of treatment (and is a bit tough to treat), while E. coli or even another cause would require something different.
On other air sac issues, people deflate the air sacs. But do we do it with this one? Tough call. Because they seem to be paired (as the clavicular air sacs are indeed paired) I'm not sure that I'd want to make that call without a really good experienced avian vet. As he's improving, I wouldn't want to risk it.
Now - here's a shot in the dark. Both E. coli and the fungal Aspergilli are "said" to be effected by... get ready for this... cinnamon. There are tests that seem to indicate that cinnamon inhibit the spread of two of the common causes of airsaculitis.
This is just weird because a friend and I were JUST talking about using cinnamon in a case of birds who, despite testing, weren't found to have anything clearly bacterial. And we were talking about using cinnamon.
If I were you, I'd just take a shot and try adding a tiny bit of pure cinnamon into his daily mash. It seems the type of thing that must be long-term. It won't hurt him in small doses. It might help.
This is not at all the answer or information I thought I'd find, but without a causative agent to treat, and not wanting to stress this little guy further, that's what I would do if he were mine until we get more answers for him.
My brain hurts now.
I'm going to do something simple and non-taxing and let this soak in. But I'd love to hear what you think about the above.
Hug the little dear for me, please. I really want to see him get through this and be a stunning little guy.
First, I highly suspect some sort of air sac infection (airsaculitis). There are many kinds, many causes, some scary, others not so. It seems when i was doing research, all I find are the scary MG related ones. There is no indication that this bird has MG and, given his absolutely sad state of health (which you're kindly repairing) if he did, he'd just flat die. So I'm ignoring MG related airsaculitis as a backburner item now and suggest that you backburner-it too.
Not that we should forget it - but there are other things that seem quite more likely.
Here's the weird part, and I should know this as my bird is experiencing it right now.
If there is a (get this) broken bone, particularly the humerus, the air can inflate the adjacent air sacs causing inflation. In the case of my bird (who had an amputation causing a forced cut of the bone which is leaking air into the adjacent tissue) this is supposed to cease over a week and deflate. Thankfully it's happening earlier.
Flock history: you initially suspected this baby as having a fracture. But I don't recall that it was the humerus. If you look at this skeleton, which bone did you suspect he broke:
http://www.krassesrudel.at/forumbilder/thecoop/figure3.gif
I just thought it an *extremely* odd coincidence that broken bones were brought up.
Now, in practical reality, one of the causes of airsaculitis is E. coli. E. coli is a coliform bacteria, present in all healthy birds in small amounts, but can be spread through feces, bad environmental conditions, and blooms in birds with depressed immune systems and bad caretaking. If any bird had those conditions, this little guy did! E. coli invasion of the air sacs sometimes result in a yellowed exudate within the air sacs. Do you see anything like this? (Of course that's probably observed through necropsy and we don't want to see a necropsy of this baby for another 10 years!)
Another issue, which wouldn't surprise me, is that aspergillosis also can cause this. Aspergillosis is a fungal issue, and often results in poor environments. Again - fits the bird. Though I think it's usually associated more with nodules in the lungs than the clavicular air sacs I believe you're seeing.
The problem is that if this is airsacculitis, it could have come from the bone and spread to the air sacs, or it could originate in the air sacs and possibly infect bone. I think he has other more pressing issues, but it would be nice to treat this.
Can you tell me whether this is new - this pair of airsacs, or do you think they've been like this the whole time you've had him?
The other issue is that to treat, what do we treat? We don't know the true causative agent. Aspergillosis is fungal and requires one type of treatment (and is a bit tough to treat), while E. coli or even another cause would require something different.
On other air sac issues, people deflate the air sacs. But do we do it with this one? Tough call. Because they seem to be paired (as the clavicular air sacs are indeed paired) I'm not sure that I'd want to make that call without a really good experienced avian vet. As he's improving, I wouldn't want to risk it.
Now - here's a shot in the dark. Both E. coli and the fungal Aspergilli are "said" to be effected by... get ready for this... cinnamon. There are tests that seem to indicate that cinnamon inhibit the spread of two of the common causes of airsaculitis.
This is just weird because a friend and I were JUST talking about using cinnamon in a case of birds who, despite testing, weren't found to have anything clearly bacterial. And we were talking about using cinnamon.
If I were you, I'd just take a shot and try adding a tiny bit of pure cinnamon into his daily mash. It seems the type of thing that must be long-term. It won't hurt him in small doses. It might help.
This is not at all the answer or information I thought I'd find, but without a causative agent to treat, and not wanting to stress this little guy further, that's what I would do if he were mine until we get more answers for him.
My brain hurts now.

Hug the little dear for me, please. I really want to see him get through this and be a stunning little guy.