Override an url with hook_menu_alter : problem with the file path
You can set the file path explicitly:


  file path: The path to the directory containing the file specified in "file". This defaults to the path to the module implementing the hook.


So your code might look like:

$items['node/%node/delete']['page arguments'] = array('myfunction', 1);
$items['node/%node/delete']['file'] = 'includes/custom_node_delete_confirm.inc';
$items['node/%node/delete']['file path'] = drupal_get_path('module', 'mymodule');


Be careful not to completely overwrite an existing router item unless you absolutely need to, in your example you're removing the required access callback/access arguments, and also the title; instead only change the values you need to as in the example above.