Content error in 3.9

I changed upload locations to a new location and because of doing that it has broken the wp-settings.php on wordpress 3.9 causing a massive formatting issue on my site with my theme. I was checking the differences between the 3.8.3 and 3.9 and it appears that line 213 (below) seems to be the biggest culprit. Is there a way to set up a work around to keep my uploads directory and possibly keep my plugin path the same as well and not cause this formatting issue on my site? Thanks for the help!

diff settings

166a167,168
> $GLOBALS[‘wp_plugin_paths’] = array();
>
175a178
> wp_register_plugin_realpath( $network_plugin );
209c212,213
< foreach ( wp_get_active_and_valid_plugins() as $plugin )
—
> foreach ( wp_get_active_and_valid_plugins() as $plugin ) {
> wp_register_plugin_realpath( $plugin );
210a215
> }
251c256
< $wp_the_query = new WP_Query();
—
> $GLOBALS[‘wp_the_query’] = new WP_Query();
259c264
< $wp_query = $wp_the_query;
—
> $GLOBALS[‘wp_query’] = $GLOBALS[‘wp_the_query’];
273c278
< $wp = new WP();
—
> $GLOBALS[‘wp’] = new WP();
334c339
< $wp->init();
—
> $GLOBALS[‘wp’]->init();