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> Is it just a backbone which you can render invisible to the end user?
What you can do to start is just build out all of the different templates you are going to need in pure HTML/CSS/JS and *then* migrate them over to WordPress. You’ll likely have a few templates: Home, Regular Page, Any Custom Pages, Contact Page, Blog Listing, Single Blog Post, etc.
Make sure you code all of those up and then you can turn it into a WordPress ‘theme’.