What could cause continuing pain, pressure and difficulty breathing in nose 3.5 months after septoplasty? Recent CT shows no infection.

Persisted deviation. If the primary reason for septoplasty was deviated septum, or correction of collapsed septum, the deformity may have persisted or recurred.It could be a chronic septal hematoma or may be internal valve problem.Your best course is to go back to your original surgeon for help, or fiind another one who can help you.
Swelling of the lini. I wonder what meds you are taking: you may be having an adverse reaction to some you have been on for a while. Otherwise i'd say avoid all (all = 100 %) wheat, rye dairy, and soy. Betcha you get better if you do this 100 %. Hrs. www.thepmc.org.
Retained splint? It is possible that one of the splints used during the first week to stabilize the septum was inadvertently left in the nose.