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I don't have experience with it, but we recently had a really nasty wet cough with lots of snot and were prescribed a nebulizer with albuterol. The pharmacist said it could increase her heart rate which might make it harder for her to fall asleep (it was to be done before bed time because it was the worst overnight) and that we could give a small dose of children's benadryl to help dry up the mucous and make her more drowsy to counteract the alertness from the albuterol.
I don't love to medicate my kid, but this was one case where I felt alright giving her both medicines. Could you call the nurse back and see if occasional benadryl might be helpful in drying the mucous and aiding in drowsiness? Maybe just at bedtime, and wing it with potentially weird naps?

@scg00387: Hope it helps and that he finds relief soon! Ellora is just now (more than a week later) losing her cough. I think it was potentially croup but not diagnosed as such, she had the 'barking' cough for only one night though. She still has clear snot running from her like a faucet and has a mucousy cough here and there. We haven't done the nebulizer/benadryl combo for several days though as it has cleared up a lot.

I second @Sweet T: mine has had multiple doses of emergency steroids and epinephrine for croup and doesn't affect her sleep. Everything else does, though!
I have also found croup to be a good time to throw rules out the window and allow more TV time than usual.