I would not worry about moving the code, I would use html5 elements to tell the search engine what is what. Such as

<header>

<nav>

<menu>

<aside></aside>

</menu>

</nav>

</header>

From my memory Google does treat urls as case sensitive.

Best to keep al urls as lower case.

I don't know that Google does ignore it. anyhow Bing does not http://perthseocompany.com.au/seo/reports/violation/the-page-contains-multiple-canonical-formats

Are they identical, you say the search equivalent, I just wouldn't treat search engines any different

Well then, yes I would be concerned, you are serving up different content to users, that is cloaking.