I guess I'd like to have a more thorough understanding of how bonuses are calculated.
How is the system different than Civ 4? In 4 you would have the base bonus, and the improved bonus which includes the base bonus I believe, and then the actual improvement's bonus added on top of that? In CiV there is the tile value, then the resource bonus is added to that without any improvement, and then the improvement bonus is added on top of that, but the bonus varies not by the improvement, but by the resource without the improvement's value added? I'm sorry if I am not explaining this clearly...
I try to do the math with various tiles and it doesn't always work out. For example, a mine is supposed to add one production to a tile, but when I start with a hill grassland tile with two production, it adds two production instead of one without a resource.