Two things I'd suggest.

One is to choose a shake that's closer in color to the main siding. When using so many materials, to keep them from being overwhelming and shouting at you so much, you want a tone on tone effect rather than having the gables jump out at you because of the contrast. It's the textural difference that makes it work, not the different colors. That would be a Victorian influence, not Craftsman.

Two is to use the stone only at the natural foundation line of the home, not the high waisted look. Or, take the stone off of the garage and use it for the entire first floor of the home. That would be a natural break line for it's use.

I don't know what color windows you are choosing, but I think that something in an actual color like a red for a splurge, or maybe just a standard bronze for budgetary reasons would work. Dark to echo the roof color and tie it in with the rock from top to bottom. I know red doors are ubiquitous, but I also think that a red door would be really handsome with the color combination you have happening. And the facade is kinda crying out for something other than brown or beige to be used on it.

Live_wire,
Thanks for the suggestions. I wholeheartedly agree about the stone, unfortunately we don't have a choice as the matter is dictated by covenants. It's a great neighborhood in everything but architecture.

I'm torn about simply using the same shade for both lap siding and shakes--in part because the gables on the side of the house won't have shakes, and I don't want the front to look too different.

The house will have white trim and white windows. But I do like the idea of a striking door. White vinyl windows for budget, and we like the look of white trim. Does that change your suggestions above? Thanks

Are there any other colors to view...or do you just want us to tell you what we think of these particular choices?

I like the stone! I don't know if I'd choose a black roof, but a very dark charcoal gray might be nice. The siding or the shakes...but they seem to clash with each other. Like you tried to match them, but didn't quite make it. Of course, looking at them on a computer is so subjective...they might look great together IRL :)

LL, I think we're fairly set on the main color, the question is mostly what to do with the gable ends and roof.

What about just doing a white band and then the same siding above it on the gable ends? I think this makes it a bit less cluttered of a look?

This should be roughly the right colors, but I'm not sure about the roof (so hard to reproduce with angles and such):

Or with colors would look something like the scheme of the house below:

This house is for sale in my area. The style and colors are similar to what you're doing.

Close up of the back with a better view of the siding color.