It is difficult to answer your question, as I guess your doctors would agree. I suppose there is some sort of over-all systemic thing that could be going on...but you have ruled out some things already.
I would NOT underestimate the impact of emotions and stress in your problems. It is easy to have things snowball. It is a well-proven fact that how one handles pain can have an impact on the amount of pain one experiences. It is a vicious cycle, as the more stressed, concerned and worried one is over their pain, what is causing it, whether it is something really serious, etc. the more it hurts...and the more it hurts, the more upset one becomes.
Some of your lifestyle may be contributing to your symptoms. Sitting in front of a computer for hours can cause eye problems, headaches, etc. Sitting with poor posture, or in a position that is not ergonomically friendly can cause issues. The more tense one becomes, the more the shoulders creep up toward the ears, the more the muscles tense up, the worse off one becomes.
I would encourage you to work with the physical therapist to develop some strategies that you can impliment at your job -- make a point of getting up every hour or so to take a quick walk, roll your shoulders and neck, etc., give your eyes a break. I remember a few years ago my daughter worked in an art museum cateloging a a new collection of photographs. She was looking at slides on the computer all day long and as a result, developed some problems that took her to the ophthalmologist. He thought all her headaches and eye problems were a result of starring at the computer screen all day. He had an explanation which was fairly technical but made sense. He advised her to change her focus every five minutes or so -- just by blinking and looking off into space for a minute. She made a point of doing this, and within a week all her problems went away.
I would suggest you work with your PT to develop an exercise program that you can do every day at home that will result in increasing the strength and flexibility of your back, core and legs. Rearrange your work station so it is the best it can be ergonomically. Get a really good chair if you don't have one already. Some offices will bring someone in who specializes in ergonomics. Otherwise there is lots of information on the internet.
I would also suggest you invest in a CD on meditation or relaxation. You can look online to see the variety that is available. I particularly like the ones by "Belleruth Naparstek". She makes them for all sorts of health issues, etc. Her voice is relaxing. You listen to it right before falling asleep at night...and I think it works magically as you sleep!
I used hers on preparing for surgery before my last surgery and I was so calm going into surgery that everyone commented on it and were impressed. As a result, I came through surgery without any issues with blood pressure fluctuations, etc...made my anesthesiologist's job easier. I had little pain afterward and the recovery was easier than after my other two spine surgeries. She made me a believer!!
I would suggest you eat a healthy diet. Food allergies "could" be contributing to your issues. Drink lots of water. Get plenty of sleep. And have faith that you will get better.