The build

The closest I've come to building my own house was turning a small, single storey, 3 room cottage into a 2 storey one. I wanted it to be as self-sufficient in energy as possible. An architect friend helped me to draw up the plans and, after a few hiccups, I was granted planning permission. My extreme "green" ideas cost me a fortune and I learnt lessons from doing it that, maybe I wouldn't do again. 
Solar panels on the roof were worth having although, as I didn't live there all the time, I didn't use all that was generated and it went into the grid. They generated only on sunshiny days which was usually when I would be outside not using power! Slow cookers helped to use a bit!. I think you can get batteries to store the surplus energy now and that would be good.

All the rainwater from the roof was stored in an underground tank. When full, it overflowed into the public drains. Each time a toilet was flushed, a pump would kick in to refill the water in the cistern - this was good and my water meter bills were very low. I could have added a hose pipe for watering the garden - but didn't bother. If the water level in the tank was too low, a float valve triggered mains water to top it up. It all worked fine until the pump jammed and kept pumping water out into the drains and drawing water in from the mains - for a week whilst the house was empty. Took me months to repay the water bill. 

I had 2 woodburners , one up and one downstairs but had to build chimneys in the roof for the smoke and vents in the walls for ventilation. 

It was an interesting experience but would think twice before doing it again. 
Your new build, with a blank canvas, should be much simpler.