The photo in post #6 kind of inclines me towards them being feather cysts/ingrown feathers. It's hard to judge from a picture though. So if a vet visit is not possible, and that would be my first recommendation both for these and to positively ID your respiratory infection, my inclination would be to try to clean one out, like the one in #6 and see what is in there, using small tweezers or what ever works to get to it. See if there is feather matter in there, or any pus. Then rinse it out well with chlorhexidine and put some antibiotic ointment, like neosporin on it. They look fairly small in the pictures, if they were large I would be more reluctant to do it myself as there could be a lot of bleeding. Otherwise, if the bird is not acting sick, I'd probably do a wait and see to see if more develop or if they stay stable or get worse. Maybe someone else will weigh in with other ideas of what is going on. Sorry I can't be of more help.
Here are some links on feather cysts for reference, so you can see if this looks like a possibility.
http://www.poultrydvm.com/condition/feather-follicle-cyst
https://vcahospitals.com/know-your-pet/feather-cysts-in-birds