Firstly, Mill the flour.
To a stand mixer, add water, butter, maple syrup, Carraway seeds, and sea salt, then mix ingredients to combine.
Then, add flour and active dry yeast to the stand mixer, and start to mix until all the dry flour is combined.
Cover and let it sit at room temperature for at least 15 minutes, up to 2 hours to allow the fresh milled flour to absorb the liquid, and also for the bran to soften.
Start the kneading process. This could take anywhere from 7-25 minutes with fresh milled flour. This varies greatly, so the best way to check if the dough is done being kneaded, is to check for a window pane test. You are just looking for nice stretchy dough.
Once the dough is nice and stretchy, remove half the dough and place in a buttered bowl that is big enough to allow the dough to double, and then cover the bowl to allow the dough to rise. This will be your light rye portion of dough.
The other half of the dough will be the dark rye portion. So, to dark dough portion, add molasses and cocoa powder. Knead those ingredients in, just until combined. (Don't over knead the dough.) Cover this dough and allow it to rise.
I go by my light dough, and watch for it to double. This will typically take 1 to 2 hours.
Heavily butter your bread pan so your bread won't stick, then place the shaped loaf into the prepared pan. (OR line with parchment paper)
After the light dough has doubled in size, flatten the dough into a rectangle that one side is slightly shorter than your bread pan. I like to use some softened butter on my hands and work surface to shape the dough.
Then, flatten the dark dough portion to a very slightly smaller rectangle. Lay the dark dough on top of the light dough. Roll the dough up with the shorter side of the rectangle facing you. So that when the dough is rolled up into a log, it will fit perfectly into your bread pan. I like to pinch the ends of the light dough over the dark dough. Place the rolled loaf in the prepared bread pan.
Cover, and let rise for about 45-60 minutes until almost double, and puffy looking.
Preheat oven to 350*F towards the end of this second rise time.
Bake for 45-55 minutes, until the internal temperature of the center of the loaf reaches 190*F.
Remove from pan to a cooling rack, allow to cool at least 2 hours before slicing.
Slice and enjoy!