Someone might disagree with me, but I don't think it will be an issue. To some extent, it seems to me that what you're describing happens pretty regularly anyway.
Take, say, the Thesis theme for WordPress. Hundreds or even thousands of people use it. I'm sure there are businesses out there that use the same basic navigation (Home, About Us, Services, Contact) and who don't customize it very much. That means that the only significant difference is the content. I haven't ever heard of this being a problem.
A similar (though not identical) situation occurs sites my company develops for our clients We start the coding on many of them with the TwentyTen/Eleven themes, as they provide a solid base. While the sites look totally different, the core pieces of the code, the majority of the classes and ID's, the HTML structure, are the same. The only real difference is the CSS. Again, because they're small/medium businesses, they often have very similar navigation structure. So far we haven't had any trouble ranking them.
Anecdotal evidence that doesn't fit your situation perfectly, I know, but my gut feeling is that you'll be fine so long as the content is unique.
From a user experience, you might want to consider at least convincing him to change any photos out. Nothing says cloned site like identical images.