As Maniek says, "The body sets priorities, without the prior approval of the owner." Amen to that.
Lungs, schmungs. Your body knows the right order to do things in, and in its own time. Seriously -- Its Own Time. Overall, I choose Option 1, without a pathogen necessarily being involved. It could be plain ole gunk. Over Christmas I coughed and coughed, felt my thyroid vibrate every time I did it, I didn't know what I was coughing out. Two weeks later, my thyroid started working without medication. It hasn't been consistent, mind you, but this tells me it will happen. Let go of trying to control what happens. Find a dose and combo that sings for you, support yourself, settle in, and forget about it. Update in 6 months. Iodine repair is a long haul.