I remedied the problem by adjusting the seat base to be quite a bit higher (it came set pretty low from the factory). It seems like that changed the angle of my back, and there's much less discomfort now.
Overheated clutches have a rather unique smell. Since the car is so new, what you smelled may have also been exhaust parts simply getting especially hot for the first time, and maybe brakes getting hot too, depending on how you were driving. If your clutch releases were quick and smooth, there's...
When you factor in the savings on gas, maintenance, and tires, and the low depreciation with Civics, the savings wold practically pay for the Civic if you keep it for ten years.
I'm interested in hearing what the dealer says th problem is, but aside from that, leaving the car idling for 5-10 minutes doesn't sound like a good idea. Even if that practice doesn't cause damage, why not just turn it off?