Save each meta box out to a file with the code as if they were in your functions.php file. Maybe place these in a folder called meta_boxes. Then to include into your theme just include() them into your functions file
<?php
// all the code that your functions file contains
include("meta_boxes/meta1.php");
include("meta_boxes/meta2.php");
include("meta_boxes/meta3.php");
include("meta_boxes/meta4.php");
// As so on....
?>
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