Pagination in custom loop [duplicate]

Question

I thought I know how to add pagination to a custom loop and I've seen these questions and tutorials:

• Pagination not working with custom loop
• http://weblogtoolscollection.com/archives/2008/04/19/paging-and-custom-wordpress-loops/
• http://www.wplover.com/756/how-to-get-custom-wp_query-loop-working-with-pagination-and-wp-pagenavi/

but for some reason it doesn't work at this time. I created myfile.php, named it to "My Page Template" and set that to be my front page in Admin Panel > Settings > Reading.

$paged = (get_query_var('paged')) ? get_query_var('paged') : 1;

$args = array(
    'post_type' => array('my_custom_post_type'),
    'paged' => $paged,
    'posts_per_page' => 3,
    'ignore_sticky_posts' => 1
);

$wp_query = new WP_Query( $args );
var_dump($wp_query);
if($wp_query->have_posts()) :
    while($wp_query->have_posts()) : $wp_query->the_post();
        // show post
    endwhile;
endif;

next_posts_link('Next posts');

wp_reset_query();
wp_reset_postdata();

What happens:

• Front page shows 3 posts as expected.
• "Next posts" link is shown and points to http://example.com/page/2/ as expected.
• While I'm on http://example.com/page/2/ it shows the same set of posts and "Next posts" link points to http://example.com/page/2/ which is not what I want.
• var_dump($wp_query) shows public 'max_num_pages' => float 8.
• var_dump($wp_query) shows public 'found_posts' => string '24' (length=2).
• var_dump($wp_query) shows public 'is_paged' => boolean false.
• var_dump($wp_query) shows 'paged' => int 1 (when I'm on page number 2).
• When I'm renaming $wp_query to $my_custom_query then "Next posts" link doesn't show at all.

Is there anything else I should do here?

UPDATE: I managed to set proper $paged by changing $paged = (get_query_var('paged')) ? get_query_var('paged') : 1; to $paged = (get_query_var('page')) ? get_query_var('page') : 1; but it still shows a wrong navigation link.