Hi Gil,
In answer to your questions.
1. Yes, we modified certain stages as necessary to find accommodation or to shorten the distance. We typically arranged for a taxi to meet us and take us to wherever we needed to go (sometimes it was a train). Typically it was because there was no lodging available but occasionally we simply called it quits because we did not to walk 20 (or so) miles. It certainly is a cost but was well worth it when we felt the need to put the brakes on. We always found taxi, train or bus schedules readily available either by chatting up locals or going online.
2. The snow was never over the tops of our mid height boots, and the temps never dropped much below freezing when we were walking. That being said in winter months anything is possible. You could have blizzard conditions and sub freezing temperatures. There are sections of this route where you will definitely be alone. If you are under prepared you will be assuming a certain level of risk that could come back to haunt you. The best advice is to always be informed regarding the weather. Talk to the locals before setting out on potentially dangerous sections (Basque Country) and be ready to lay over if the forecasted conditions look unfavorable. Seemingly straightforward hikes can become a nightmare when you run out of visibility, daylight and the snow is deepening around you. But with proper precautions the route is doable anytime of the year, but perhaps not on the very day you might want to do it. There are always weather events that will close any trail. Just be cautious and understand your limitations, and don't push your luck.
3. I used a hard shell jacket with merino wool sub layers. I also had a very lightweight down jacket that could have been used as an additional layer, but I never needed it. I did not use long underwear bottoms. No need.
Happy planning and buen camino,
John
