L.B.
Well I had a projectile vomiter and he too had acid reflux so that could be a possibility. It's certainly worth looking into and going on a trial run of meds if you are game.
As for the ear infections, I would recommend following up with an ENT. Only reason being is that my kiddo only had 2 ear infections and 4 peditricians completely MISSED that he had fluid on his eardrums and couldn't hear right...it took a speech therapist to actually diagnose it because of his delayed speech. What the pediatrician might be seeing is only on the surface where the ENT can see much further into the ear...I would certainly check into that. Ear infections are typically the most logical thing I would think of that would be keeping him up.
Another idea you might want to try if you haven't already is some kind of white noise in his room...a fan, humidifier, space heater, even a small radio/CD on repeat...SOMETHING that will make noise constantly throughout the night. I found that my kids always slept better with something like that. Also, my daughter was really fond of the Fisher Price Aquarium that we attached to her crib...we would hear her at all times of the night pushing the button for the music and lights...she found it really comforting...so much so she wanted me to attach it to her big girl bed when she moved from the crib.
Finally, is it possible he might also be cutting a tooth? Stick your finger in his mouth and run over his gums...if you hit a sensitive spot you might have your answer there...Orajel and some Motrin will help get him down for the night in that case. Hope something helped here.