Middle, right-side back pain when inhaling deeply

Please ignore the "Topic" category since I could not find a match.

In July 2008 I had a small case of pneumonia in my lower left lung.  This was cleared up by August 2008 however I had some pain in the middle of my back on the right side.  My doctor indicated that this was pleurisy.  The pain from the pleurisy was virtually gone by the end of September.  I had been taking Aleve every day to help reduce inflamation (inflammation).

However, in early October the pain made a comeback and through today it remains.  I can feel it mainly when taking deep breaths.  The pain is mild and it is not constant.  I dont feel pain when sitting watching TV or using the computer or eating. I also feel pain if I intentionally tense the muscles on my right side.

Chest X-rays (two of them) have shown that everything is normal.  I continued taking Aleve and waiting another 6 weeks (resting, working, no exercise) but the feeling is the same.  I think the issue is muscular because stretching helps alleviate the pain and I noticed that after taking a hot shower the pain is virtually gone.

I would like to get some opinions from the doctors on this forum.  If it is muscular then why does the area still feel sore/pain after the recent 6 weeks I have been resting?  Is it possible that pleurisy can last for 5-6 months and come and go?  Any other ideas?

I have stopped taking Aleve since I feel it is not helping my back and to give my stomach a break.  My doctor is suggesting either physical therapy or a CT scan.  In place of the PT I have been stretching multiple times a day and massaging the area.  I am hesitant on getting the CT scan unless absolutely necessary due to radiation concerns.

I'm 39 years old and was extremely healthy prior to this, no smoking/drinking, eating right, and working out 3 times a week running about 10 miles/week.

I appreciate your professional responses.

[Thorninside]

I know that you were asking for an expert's opinion, but I may have an answer for you.  I get those sometimes and they seem to come from nowhere.  I can't think of anything I did to cause these attacks.  
I do go to a chiropractor on a regular basis to prevent degienerative disc problems and chronic fibromyalgia pain in my shoulders.  He has been a miracle worker.  The pain is not gone but my range of motion is almost 100% better.  
One day I had one of those pains on the left side of my mid-back that ran to just under my arm.  He told me that I had a rib out of place, adjusted it and I was good to go.  It still happens every so often and he adjusts it and I'm fine.
Just a suggestion.