My sister had a very generic back yard/patio. A few years after moving in they decided to re-do the entire back area. She had 3 landscape firms draw up plans, explaining that she wanted each to provide their best ideas and bid on the project. She picked the one that best fit her needs, but did end up incorporating some ideas from all 3.

Not sure what you mean by "Craftsman flair." The Craftsman style is for much smaller houses, kind of squarely planted on a foundation, (well under 2000 sq ft) with porches, wood features, small dorners, pillars, often one-story, cottage garden, steps, certainly no dominating garages out front or big wings on the side. Your house has features no Craftsman house would have. Cozy colors that work with a small Craftsman would be too loud for your very large house. If you want a cozier look to your house, unless your house needs a paint job, devote your budget to beautiful front gardens instead of trying to get "Craftsman flair" on a house that is the opposite of that style.

I would paint the courtyard wall the same as the body of the house. No stone. Cacti or other drought tolerant plants in front of the wall would look great.

It looks like you're in a hot, dry climate. Do you really want to paint your house darker? Above all, the exterior of your home should function well. "According to the National Renewable Energy Laboratory (NREL), dark and dull colors on a home’s exterior absorb anywhere between 70 to 90% of the sun’s energy. Once your home absorbs that energy, it transfers most of it as heat inside via conduction. "