1. Go to a body shop. The one I went to based prices on time and materials like a repair. I doubt the dealership would do the same. Besides, the bodyshops specialize in paint and body work.
2. Again, mine charged by time and materials specific to each part painted. I'm not sure if all bodyshops work the same. I doubt it would cost too much more to buy parts individually and paint them separately. One caveat, however. If the time span is too great and the car is going to see a lot of sun, you might have fading which would make the parts harder to color-match.
3. The biggest challenge in painting the aftermarket parts is to make sure they add a flexitive (I believe it's called) to the paint. It lets the paint move with the part as it changes shape due to temperature or just movement. Make sure they'll warranty the installation if you just use body tape. Mine didn't, but since the hood scoop is right in front I'll see it if it starts to peel off. You migh miss a side scoop if it falls off. If you need to prep and paint the surface under the part to be installed, add the clearcoat first, then the part over. Don't add the part and then paint and clearcoat over. As the dissimilar materials change from temperature, the paint will chip. In my case, I had the hood painted and clearcoated, then added the previously painted and clearcoated scoop. Again, if it comes off, I don't have this ugly bare spot until I get the scoop re-installed.
Just my two cents.