Create an Array of Specific Custom Post Meta

If I’m understanding your issue correctly, and if by ‘project title’ you mean the content of the post_title field, then it’ll look something like this:

$post_data = array();

$my_query = new WP_Query( $whatever_your_args_are );
if ( $my_query->have_posts() ) {
    while ( $my_query->have_posts() ) {
        $my_query->the_post();
        $post_data[] = array(
            'project_title' => get_the_title(),
            'latitude'      => get_post_meta( get_the_ID(), 'latitude', true ),
            'longitude'     => get_post_meta( get_the_ID(), 'longitude', true )
        );
    }
}

echo json_encode( $post_data );

I changed your example just a touch so that the JSON object would have the values keyed nicely (project_title, latitude, longitude) instead of the more opaque numerical keys. I’m also assuming that you’re using WP_Query to query and loop through the posts. If not, you can replace the WP_Query stuff with a loop over whatever content you’ve pulled from the DB.