Don't worry about Canadian Customs giving you grief in YVR. In an absolute worst case scenario that will cost you an hour in secondary (because of the lack of traffic at that hour) and will release you into Canada by 4am at the latest. The US INS will open up around that time as well, so you shouldn't have too much wait time.

They key to avoiding scrutiny from Canadian Customs is to answer "TRANSIT" when asked the purpose of your trip and to fill out your customs card saying "1 DAY" for duration of stay. If they ask for details then provide them of course, but deluging them with info at the start is a sure way to confuse them and get yourself sent to secondary.

Don't sweat the YVR part of it. The Canucks tend to be very anal at times, but the end result is usually fine. I'd be more concerned about JFK.