Well im not sure about the side moldings, but i put my factory spoiler on my 07, its the same as yours. I bought mine on ebay, but beware, most do not come with a templete, u will need this so u can find out where to drill your holes. And make sure your templete line up with your spoiler. U can go to the dealer and they will have them, its just a piece of paper with the outline and drill marks on it.
you got an 06 so I don't think you would have a different shade because it haven't being under the sun for too long. but a lot of people did remove the side molding and i think I will do it too this summer