Le Comptoir’s baguette is sourdough made from freshly-milled whole wheat.
Each loaf is made using our 26-year-old sourdough starter and freshly milled organic whole wheat flour. When booking your reservation, please indicate in the Notes section that you would like to purchase a loaf, and we will have it ready for you at the end of our dinner service. Our bread takes two days to prepare, so we will not be able to accommodate requests that have not been placed ahead of time.
Ok, but I still don’t read OP’s post as necessarily asking for bread that is sourdough and made from freshly-milled whole wheat. An equally likely interpretation is that OP is asking for bread that tastes as good as or better than Le Comptoir’s, notwithstanding how it is made. Maybe OP can let us know.
What is her opinion of the usual suspects? Bub & Grandma’s makes what I think is the best, most consistent loaf in the city. Some of them are 100% whole wheat, I think, though it isn’t easy to find a list online.
Clark Street also has a loaf that is specifically whole wheat, organic and California-grown for whatever that’s worth. I like their bread in general too.
Seed, which Robert linked above, is good and unique - much more dense, in my experience, and perhaps a little more sour. I don’t like them quite as much as those other two but it may be more to your spouse’s taste.
Friends and Family from @hppzz is another good option.