One of the ways to use rough cut lumber is to build a timber frame house. Is this what you are thinking?
After you build the frame you can put stress skin panels on the exterior of the frame, leaving the frame exposed for the interior. The stress skin panels come in various thicknesses, and they are super-insulating because of their thickness and because the insulation is not interrupted by studs as in conventional framing. I understand that the panels are now made with conduits or raceways for running electricity and plumbing.
The panels can be made with drywall on the interior and plywood or a similar material on the exterior, making it easy to complete the interior and siding work.
You are already planning to use non-standard windows and doors anyway...
There are lots of books on the subject, and there are schools that teach you the ins and outs of timber frame construction.
I've always wanted to build one for myself, but I don't have the time, money, or forest!
Good luck and keep us informed about your progress.