As for a color scheme, I would make sure that the roof color is the darkest color in your exterior color scheme. I would ignore the color of the siding on the backside or paint it to match the body of the house. Per your drawing, you have used the shingle roofing material on the pitch of the second story door, I would make sure that the you use the same materials.

Since you have indicate that you like grey, I would go with a monochromatic grey color scheme and have the roof be the darkest gray color or almost black.

I think a deep burgundy would look great with this scheme.

As for the number of different shades of grey to use, it really depends on much you want to highlight the details that you are to the house. I would first pick a roof color then look for a primary shade of grey to cut with white to make the other shades.

Also, it appears that when you remove some of the siding that you will expose what appears to be a cinder block foundation, which you'll have to decide whether to paint it or not.

Also, you'll need to decide how you want to finish the new steps and base of your new entry stoop. Will you use stone or stained cement? This will need to be considered in your color scheme.