Framers installed shear walls, seismic hardware, and the entire roof with the wrong nails. What now?
There are several issues you’ll need to resolve: 1) was a Building Permit obtained, 2) was the contractor licensed and bonded, 3) is the design correct, 4) was the installation incorrect, 5) is the installation unacceptable 

1) This project requires a Building Permit. If one was not obtained, who is responsible. (The contractor will say the home owner is responsible because they are doing just a small part of the construction.) Obviously footings were poured, etc. and those should have been inspected and approved. Now, the framing should have been inspected and approved or rejected. Did the Building Inspector approve the framing? If not why not?

2) The contractor is required to be licensed and bonded. If he was not, why not? 

3) Was the design correct? The designer needs to confirm that he did not make a mistake and is v CCB orrery for this installation. Designs are not random. They follow specific guidelines laid out in the Building Code for your area (region). You don’t want the design to be unreasonable, or if it is, then why the “extreme” design. 

4) Perhaps the framing was incorrect. You’ll need the designer to confirm the design is correct AND the construction needs to be “fixed”. (“Fixed” May mean “replaced”.) Get their determination in writing. That way, you are not being unreasonable, just following your designers recommendations.

5) You’ll need a third party to review the installation and determine that it is unacceptable. (The contractor will obtain their expert witness and they will say it is acceptable.) Not every project is designed to the maximum performance of nailing, blocking, etc. Often, a lesser nailing pattern, smaller nails, etc. will still provide “adequate” structural performance. Your expert will need to show how the installation is defective AND make a recommendation for the “fix”.

Btw, there is a Builders Board that license contractors in your state that can referee this issue if you do not want to go to court. 

Summary:

Just because it was not installed correctly, doesn’t mean it needs to be replaced. Do your homework and get everything in writing.