Search "color block" in Exterior photos on Houzz for examples of multi colored inspirations. Here are I few I thought were interesting.

any of these colors should work. I also like darker trim color options. any of the sage greens or the warm colors will work. you could also do a combo of 3 colors. leave the stone work as is, and work around it. bringing in some darker tones for contrast would look great. I suggest looking at pics of craftsman bungalows and other split level brick/stone exteriors, to get ideas. I would not paint everything one color. that will be disastrous. No pink/peach shades. no light gray, and the green should be a nice sage tone, not a mint green. I like the one in the lower right corner, using the adobe red for the door

Did not see celerygirl 's mock-up before I did mine, but they are very close. I didn't indicate in my mock-up, but I would also paint the dark brown wood siding the same color as the stucco.

Not necessarily. I was just thinking match three windows with three windows for symmetry -- and get wider windows but fewer of them. Not sure about the cost difference with that. Since your contractor already has the size, you might also ask for a quote on three windows and the installing the second vertical framing. If you add four windows -- two double hung -- you'd have narrower windows -- and still have vertical framing between the two pairs of windows. Do some math and see how narrow those windows would be before you decide. Make sure your contractor knows you want to fill the entire window space between the bricks with windows and framing. Understand where that framing would be -- how much will be wood and how much glass and actual window and the cost difference between any options you're considering. While It might even be possible to use only two windows in the space and fill the width with mostly windows and little vertical framing, however, really large windows may have the potential to begin to have a commercial building vibe. Just to be sure your windows would not be that large, do go by a building supply store and explain to the clerk what you're considering and see if he/she will set two windows that size side by side for you to look at.