There are many possible reasons for swallowing and breathing problems. Anything in the neck that can press on the trachea or respiratory airways can bring on these kinds of symptoms. Have you noticed any stiffness in the neck or difficulty moving the head and neck?
Any other symptoms such as choking, new episodes (or increased episodes) of snoring? Any numbness, tingling, or electric shock sensations down the arms? These would all be symptoms to report to your physician even if you are not having the symptoms at the time of your examination.
Perhaps keeping a log of what you notice, when you notice it, and any other observations you think are important will help. This type of record can bring to light a pattern or trend that can offer the physician some diagnostic clues.
You didn’t mention any imaging studies. Have you had an X-ray, CT scan, or MRI? Usually the first step is X-rays as they are the least expensive and often provide helpful information. Your age, sex (male or female), and general health may offer some additional clues.
A recent study from the Netherlands has identified more cases than expected of dysphagia (difficulty swallowing) and airway obstruction (difficulty breathing) from a condition called Diffuse Idiopathic Skeletal Hyperostosis (also known as DISH). Until now, it was believed that DISH was a rare cause of compression of the esophagus and trachea.
With DISH, the ligaments around the spine turn into bone causing pain, stiffness, and loss of motion. Compression on the soft tissues in the neck can produce the kind of symptoms you are describing. Muscle tension, anxiety, tumors, bone spurs, and spondylolisthesis (shift of the vertebrae out of their normal position) are other common causes of the symptoms you describe.
One other approach you may want to consider with this problem is to seek a second opinion. With a little more time and a record of what’s happening (your log), a more precise diagnosis may be possible even with symptoms that seem to come and go.