Good morning, Mystiejm!
I am so sorry that you are going through all this! There is nothing worse than feeling like you are struggling just to take the next breath! I have asthma, and I have to watch my peak flow carefully so that it doesn't drop too low. Sometimes I am having an asthma episode and don't realize how bad it is until I check my peak flow, and then I have an "aha" moment and say, "no wonder I have been feeling so bad"! I think sometimes I adjust my breathing, or I am so used to coughing that I let it go until my airways are so restricted you can't hear the wheezing at all and it isn't until after a breathing treatment and the airways open up a little that you can hear it. But that's asthma and your doc will be able to sort that out for you.
That being said, I also understand what you are describing because I have experienced this too. I have recurrent pleurisy and pneumonia and it took a while to sort it out because I do have asthma. Anyway, for me, in addition to the asthma, the shortness of breath, lowered peak flow, and poor pulmonary function has also been linked to weak chest wall muscles as a result of overlap syndromes within the Lupus umbrella (for me they are Myasthenia Gravis and Polymyositis). Remember that everyone is an individual and autoimmune diseases affect each person differently...so what was the case for me might be different for you.
It is very good that you are seeing a pulmonologist because he will be able to detect, through the pulmonary function tests, the difference between asthma which is due to restricted airways, and weak chest wall muscles, which keep you from breathing properly and can lead to fluid buildup in the lungs and possibly pneumonia. There are exercises you can do to strengthen those muscles until whatever is causing the problem gets under control, and your respiratory therapist will help you with those.
I do hope this helps. Try not to worry too much and I would avoid reading all the scary stuff on the internet. Sometimes I think we have too much information available to us. My rule of thumb is this: chances are that if it is rare, it probably doesn't apply to me.