I thought it would be good to write a few things down that I have learned in my milling and baking adventures.
When I first started baking (I started with 100% WW from the beginning) I used to knead in a stand mixer but I couldn't make good bread. After a lot of trial and error, I'm making consistently good 100% ww bread from home milled flour, both sourdough and conventional dry yeast. The key for me is an autolyse combined with the right hydration (between 70 to 80%). This means that there's not much kneading required in any of my breads.
My suggestion is to start by mixing flour and water until just barely mixed/wetted, then stop. It should be mushy. *It's important that you stop, do not keeping going and developing the gluten at this stage. Cover and let rest for an hour to hydrate the bran and develop the gluten.
After an hour (or up to 12 hours refrigerated) spread the dough out flat on the counter, sprinkle on your instant yeast and salt and whatever else is in the recipe, roll it up, and knead by hand on the counter for about 2 to 5 minutes until it feels like the salt has disappeared and the gluten is developed. The dough will be very cohesive and springy and have a moist tacky surface.
If it is a sourdough, spread on the levain at this point, fold it over, add the salt, and knead it in. For active dry yeast I like to put the yeast in water and then add flour to make a paste and add it as if it was a sourdough levain.
Then continue with your bulk proof. (Optionally you can do a letter fold or two at 1/2 hour intervals during the bulk proof, just to organize the dough and build strength.) Then do a final, gentle letter fold, shape the dough, and let it have it's final hour-long proof.
Here is a really lovely video of 100% whole wheat bread using this method. You can see that after the autolyse, when combining the dough with the levain and salt she only kneads for 3 or 5 minutes minutes, just to bring together the starter and salt with the dough. That is enough to develop the gluten for a rustic bread. If I'm making a sandwich loaf, especially an enriched dough, I will knead it longer, for about 10 minutes, until the gluten is very well developed and is showing a nice windowpane.
I don't usually do stretch and folds. If the dough needs strength I give it letter folds on the counter at the end of bulk fermentation. This is especially useful for spelt and for khorasan/Kamut both of which are very extensible and need to have letter folds to soak up some of that lengthening capacity in order to be able to tighten them at the final shaping.
I don't know why developing the gluten at the very beginning mix stage messes things up so badly for me. I just know that it makes the gluten weird: it almost seems to separate the gluten from the dough into strings. It's just not good.