Mix the 1/4 cup water with the honey and yeast and let sit at least 5 minutes. I did the rest of my mixing a little differently than the original recipe(you can decide what works best for you) and added a tablespoon of lemon juice, 2 cups of water along with the flax seed and a couple cups of flour. Then I continued to mix in flour till a very sticky dough formed, about 5+ cups. I then let it rest for about 15-20 minutes.
When I came back I added the very soft butter, salt and any add ins like seeds or oats(I've read that letting the dough sit without salt or any add ins that would rip the gluten can help to strengthen it, although I'm not 100% sure). I mixed it very well by hand with a spoon and then slowly started adding more flour till I could turn it out to knead it, about 6 cups total flour added.
Then I lightly dusted my surface, turned out the dough and lightly dusted it as well. Then I set to kneading, quickly folding over the dough towards yourself and then pushing it forward with your palms. The power should come from your whole body though, not just your arms as you'll get tired very quickly. Kneading should almost be a whole body movement. I'm pretty sure however you knead is good enough but if you're not sure, you can always find plenty of videos on how to knead. In any case, I kneaded for about 10-12 minutes and then I covered and let it rest for a few minutes while I washed out my bowl and washed the dried dough bits off my hands. Then I went back and kneaded some more. You should be able to look at the underside of the loaf and see no tears in the smooth layer of gluten, if you do, keep kneading. The dough should look white with flecks of bran in it and it should be able to stretch without ripping. Check out the original recipe for a great picture of what it should look like. How I described the kneading process to my mom - knead until your arms fall off... twice. :)
Then cover and leave the dough in a large oiled bowl to rise, this should take between 1 and two hours. Depending on how warm the area where the bread is. I usually prefer to keep my dough cool so this makes the rising time longer. Make sure to let it rise as much as it will rise because this will stretch the gluten and strengthen it too. You can test it by poking the dough about 1" into the dough. If a hole where your finger was remains, it's done rising. Lightly grease or butter two loaf pans. Turn out the dough and knead a few times to get the air out. Divide in two and shape. I found it easiest to shape these by using a kneading motion in just one area and not moving the dough around, except to flip it and repeat on the other side, but do whatever works for you. You want to have a very smooth top to the dough. Once they're formed, cover and let them rise about an hour or until they're just over an inch above the top of the pan.
Preheat your oven to 350 degrees. I like to slash my loaves but as you can see I slashed a little too much in these loaves, only slash about 1/4" or just leave them plain. I like to have a pan of water in the bottom of my oven and I give the loaves and the inside of my oven a spritz of water before leaving them in there to bake. Bake 20-25 minutes. Remove them from the oven and let them cool at least 10 minutes in the pan before turning them out and cooling completely on a rack. The bottom of the loaf is very light in color but it firms up after cooling. Once you've cooled it completely you can slice and freeze it or keep it in a bag on the counter for use over the next few days. This bread is perfect for sandwiches or just toast. It's very filling and heavy in a whole wheat way, but it's not nearly as dense as most homemade whole wheat breads I've tried.