I used to have chronic bronchitis, and the cough was always worse at night and when lying down. Of course, the vicious cycle is that you cough so much you can't sleep, and you can't get stronger if you don't sleep. If this is a deep bronchial cough, the things you are doing like elevating the mattress can help. He should be coughing up phlegm with that sort of cough - if so, he should try to spit it out rather than swallow it if possible. I know it's hard for little kids to manage that!
Humidifiers can make things worse - the moisture can help with symptoms and hold down the dust, but can also contribute to the development of mold, You really have to clean them (and don't use chemicals or bleach - use vinegar). But they can help to keep things moist and lubricated.
I have to question the Benadryl to dry things up. I would think you would want an expectorant to help make that cough more productive if it's deep down. And it kind of undoes what the moisture is doing, right? If he has allergies and post nasal drip, and this is a cough in the throat only (high up) vs. bronchial, it might make sense. But you are finding your son gets relief from being propped up. So I'm confused about what you think this is.
If his throat is sore, the honey is okay but of course you have to really brush his teeth and not let that sugar sit in his mouth. But if it's a sore throat that's caused by allergy or infection or drip, vs. just the result of the bronchial stuff, the honey is probably not needed.
Have you ruled out a sinus infection that's causing post nasal drip? Is his temp normal? Sinus infections don't usually cause a cough, but I'm just checking.
My experience was that bronchial coughs lasted for a long time - weeks at a time. I'd look into a cough suppressant (to reduce the frequency and the spams) and an expectorant to make it more productive at getting the phlegm up and out. I've gotten rid of all that through immune system boosting, but I can tell you I was miserable from not sleeping and from the headache from chronic coughing. And if you're not sleeping either, both you and your son are pretty sleep-deprived and ripe for a new infection.
I guess my best advice is to decide where this cough is, and only treat that, rather than doing so many things that may be working against each other.