Maiden voyage with the Mockmill 200, and milling questions
Finally unboxed my mill and took a crack at making my favorite seeded Danish rye loaf. This is a loaf I make on a weekly basis, probably more than 30 times at this point. Despite feeling very insecure about whether I was doing things correctly, my bread turned out better than it EVER has before! The texture is awesome, the flavor profound. I'm feeling very positively about home milling.
This recipe calls for half APF (or white bread flour) and half rye. So I used half hard red wheat and half rye berries. For the red wheat, I ground it at the #1 setting and then sifted it through a #40 strainer (about a 10% extraction). For the rye I also ground it at the #1 setting and then sifted half of it through a #40 strainer. But then I questioned whether I should have sifted the rye or not, and threw all the the rye bran back in! 
For those who are more experienced with home milling, what kinds of flour would you grind at coarser than the #1 setting? Should you sift out the bran if you're trying to approximate bread flour and/or commercially available rye flour? I definitely noticed that my dough was drier than it typically is--I like how it came out regardless, but in general if you leave the bran in, should you increase the liquid?
Whole grain is not a direct substitute for AP or bread flour without changing a few things. You will probably need more water but more importantly your dough will need some time built in to absorb the water. A 30 minute to 18 hour autolyze-biga/sponge method, long retard of a slightly wet dough, poolish and autolyze .-there are so many ways to do it. If you don't, the branny bits in the crumb (which are never completely sifted out) will continue to absorb the moisture from the crumb structure after baking. The crumb will crumble with handling. Don't you just hate it when the sandwich crumbles into pieces when you take a bite!. That is why it does.
Your loaf looks wonderful! I love toothsome loaves! I have a Mockmill that attaches to my Kitchenaid. I just got it and I love it! I have only used it once but I have used a Nutrimill for several years. The nutrimill makes a finer flour but uses burrs and explodes the grain. It tends to heat the grain and flour so there are some workarounds. The stones of the Mockmill take longer to grind and the flour (even set at finest) is a tad bit coarser but just as delicious. I tend to soak my dough (as mentioned) so I have found even with a coarser setting (like a fine cream of wheat) I can achieve a very delicious, supple loaf without sifting.
Here is a lovely article by our own Stan Ginsberg on rye flours. Explore his site-he has some wonderful recipes.
Like clazar I'm using the KA version of the Mock and his point about giving the flour time to absorb water is also my experience. I let the flour and water spend 45 minutes of 'quality time' alone together (sometimes 1/2 tsp vitamin C powder chaperones their courtship) before I stir in the other ingredients. Right now around 66% hydration seems to be effective as a starting point. I will bump that up if the dough doesn't come together the way I want. If I sift the flour I generally use a much coarser sieve to isolate the coarser bits for a second trip through the stones. From my perspective the last thing I want to do is imitate commercial products. I'm looking for enhanced flavor and nutrition and I'm willing to learn how to use the unique properties of the flour I mill in order to get it. If the characteristics of commercial products are critical to what I'm baking I'll buy the commercial flour that's appropriate. I normally grind flour for my loaves at the finest setting (the KA version doesn't enumerate settings) but if I'm grinding corn for polenta or cracking other grains for a use other than bread I'll back off until I get the texture I'm looking for.
Forgive me for asking , but I just started using a Mockmill 200, and haven't really seen a settling of #1. Following the manual, one sets the mill to where the stones touch, then back off a bit; is that what you call # 1?
I have been getting a very fine flour there, and backing off makes a coarser grind for chemically leavened breads.
The resulting breads are getting raves with my customers.