How to translate a custom module template file?
The .po file must be located in custom_module/translations directory - see locale_batch_by_component function. Translation file though is only imported once module gets installed, so in case you want to reimport the file you would have to run some "hacky" drush command, such as drush php-eval "locale_system_update(array('custom_module'));drush_backend_batch_process();"

You can also upload .po file manually using Drupal's admin UI.