My 16 year old daughter has had pain in her trachea several times in the last few weeks.  It occurs in several spots.  The first time we took her into a doctor who gave her a breathing treatment and x-rayed her chest.  He couldnt find anything so he said she must be having an anxiety attack and sent us home.  The pain lasts an hour or more then goes away.  It seems to be spasms or muscle cramps because she says that it seems that her breathing is restricted and if she uses here inhaler, then she has momentary relief then the constriction gets worse.
This can be due to multiple reasons. Trachea can be affected due to infections, birth abnormality, asthma etc. I would suggest you to get lung function test (spirometry) first.