I had ear surgery and prosthesis. Two weeks later I went to hospital for 105 fever that had me admitted for a week w/intensive care for 3 days. Now I still have lung issues. Shortness of breath and if I exercise I feel like there is an obstruction on my right side between stomach and lungs. Doctors will not say if I contracted something at first visit to hospital and they have indicated my condition resembled pneumonia. Why am I feeling like there is something restricting my breathing? I have been in recovery for 3 months. Do the lungs need to regain their ability to process air? Sometimes I find myself catching by breath. It has been 3 months since ear surgery.

I strongly suggest that you go to another medical center (not another doctor in the same place) for a second opinion. I'm not saying you were given a run around post surgery, just that doctors don't always admit or spell out what can go wrong.
I can imagine infection getting from your ear to your lungs. I had chronic bronchitis for months, resistant to all the newest antibiotics, related to an infected jaw that no one could diagnose until I went to a periodontist. Sometimes you do have to shop around.
I'm not at all saying that what YOU are experiencing is in any way similar. For all you know, you have a condition totally unrelated to your ear surgery. We couldn't possibly even guess what that might be.

The 2nd stay was at a different hospital then ear surgery. Now I am thinking I should get another Dr. that specializes in rehabilitative medicine? I came away with afib and blood thinners too.

That doesn't change my response. Get a second opinion.