The $host = make.wordpress.org conditional also needs some lines from the location / block, prior to the rewrite for index.php pulled from @404-extend in http://make.wordpress.org/systems/2012/07/17/problem-with-nginx-rewrites-i-think-conflict-between/#comment-247.

Specifically:

        # uploaded files
        rewrite ^/([_0-9a-zA-Z-]+/)?files/(.+) /wp-includes/ms-files.php?file=$2 last;
        rewrite ^/core/handbook/files/(.+) /wp-includes/ms-files.php?file=$1 last;
        # add a trailing slash to /wp-admin
        rewrite ^/([_0-9a-zA-Z-]+/)?wp-admin$ /$1wp-admin/ permanent;
        rewrite ^/core/handbook/wp-admin$ /core/handbook/wp-admin/ permanent;

I suggest the various /core/handbook/ rules be pulled out into their own location block once make.wordpress.org moves to its own server block.