M., i have a 12 year old boy who went through a similar situation last year. we went to vacation and he came back sick. and for the next 2+ months he could not get rid of a cough and he had a cold/virus that lasted forever. 2 weeks after getting back he did better only to get sick again a few days later. i am super overprotective and i make sure he dresses warmly, if it's cold weather baths are at night so he doesn't go out into cold weather with wet hair, i mean, truly, i'm old fashioned. that poor kid was not sleeping because of the violent cough at night so he was tired in the morning and it was hard to focus at school. i was so mad with my pediatrician who would not even give him something for cough relief at night after so many weeks and weeks of bad sleep that i left his practice after 15 years! he was exhausted, and i thought it was cruel. my son had dark circles under the eyes.
anyway, i was pulling my hair out, and like you, thought there was something very wrong. you have done right taking him to the ER periodically since nothing has changed. let me tell you the trick i learned from a girlfriend who read about this, tried it, and passed it on to me. at night, when you put your boy to bed, get some vicks vapor rub and rub it on the soles of his feet followed by very nice and warm socks. also, put some on his chest. THE COUGH WILL BE GONE FOR THE NIGHT! obviously you don't want to do it in the daytime, he could slip. but so that he can get a good night's sleep? try it! in fact i just did that him 3 nights ago, his cough woke me up in the middle of the night, and once i walked out of the room he had stopped coughing. he slept (and so did i) for the rest of the night, cough-free.
once he gets old enough to have honey mix 2 TBSP with 1/2 teaspoon of turmeric. mix it well and give it to him. the results are immediate (better than medicine for cough). it's a great one-two punch, but the honey can be used in the daytime as well, and it lasts a few hours.
hang in there, it's even harder when they're little. and the up and down temps? are not helping at all~ let us know how he is doing!
:)