Custom Post Type homepage template

I am thinking you probably want get_template_part() to load CPT specific pieces of code. For example (from the Codex):

get_template_part( 'nav', 'single' ); // Navigation bar to use in single pages (nav-single.php)

You can then reuse pieces of code on your home page, your CPT archives, etc.

You may also find post formats useful, though I am still unclear about exactly what you want to accomplish.

Take a look at the way Twenty Thirteen (for example), handles posts formats by using content-aside.php, content-audio.php, etc

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