L.,
It still could be ears.....laying down can increase the pain at night.
I just wrote a response to another mom about the same issue. I told her to document her son's daily routine....waking, eating, nap time, eating, playing...etc. You may begin to see a pattern and notice that something he only eats at night causes a tummy ache, or he is overstimulated after bathtime, or his pj's have an itchy tag....etc.
I was crazy for a few years w/o good sleep.....when things were really bad, I just slept in the oversized recliner with my son in my arms, just so I could get a few decent hours of sleep.
The other thing I forgot to tell the other mom was to try homeopathic or herbal remedies like camommile or something like that......there are so many homeopathic remedies for kids now....google it and I'm sure you'll find tons of info.