We should probably just move into the ENT's waiting room this time of year, given my son's multitude of "stuff" (6 sets of PE tubes, tonsillectomy and adenoidectomy, and airway issues). From your description, I would wonder about a few things:
How old is your son? A wet barky cough sounds like croup to me (my 7 year old has it now.) Kids typically outgrow that by 5 or 6, but not always. The ped told us today that she'd diagnosed a 12 year old with croup this week.
Has he ever had a sinus x-ray? My son has had some really nasty, persistent sinus infections that have outlasted a few courses of tough antibiotics. The sinuses get poor blood flow and there can be little pockets of infection that are hard to reach. Gross, yes, but there it is. Having a low-grade fever would make me wonder about that.
Does he still have his tonsils? Do they look swollen? Tonsillitis could be causing some of those symptoms, too.