1 - you'll have to check with the dealer on this. Dealers will charge 2-3 times the price of a factory option (in most cases), so be forewarned
2 - Sidesteps won't be tall enough to escape door dings, unless you can find some older Honda cars to park beside. Most vehicles doors open around 12"-16" off the ground and in most cases, will go over the bars as they'll mount 1-2" below the doors and tuck inside the frame. However, you can check out Summit Racing - High Performance Car and Truck Parts | 800-230-3030
or Performance Parts Online for Cars and Trucks - Performance Center
as a couple suggestions if you HAVE to get bars.
3 - Roof rails are permanently installed. Same goes for all vehicles with a roof rail system. You could remove them yourself, but you'd void your comprehensive warranty as water and other crap would find its way into the vehicle.
4 - you'd have to measure a regular wheel/tire and compare it to the compact spare underneath. You may be able to squeeze a larger tire in, but be mindful of the exhaust. If it's too close to the tire, it'll deform it and can potentially burst the tire and you'll be carting 50lbs of dead weight around for nothing. If I recall, there might be an exhaust shield around the spare already, but I haven't looked under an '09 ...yet.