Ebro,
The reserve on my judgement is over. The only thing that keeps this from being a total disaster is the the walls still stand under their own weight. I know the professional that you are using to guide you through this debacle and all I can say is he comes with the highest credentials in your area and I would heed his advice. As a matter of fact if I were to choose a contractor to build my home, he would be on my short list. He and his son are great people.
I am sorry for your misfortune and wish time could be turned back for you. This looks like a the project was askew from the beginning. Looking at your pictures I can pick out so many issues.
Please keep us informed. I doubt you are going to receive any satisfactory relief from the parties involved but it is always the first step. You need to compile a list of issues and present them to your contractor and ask for specific relief on the issues stated. This may involve some negotiations but if they are willing to provide relief then get all of it in writing and run it past a good construction contract attorney. You ICF consultant should be able to steer you in the direction of a good one.
Once again I am sorry for your project or lack there of.
ICF Contractor