Figure out Drupal 7 mail formatting

drupal_mail_example.inc

/**
 * @param $form
 * @param $form_state
 */
function lsadataclassify_keyad_route_submit($form, &$form_state) {

  global $base_url;
  // For each pm checked
  for ($i = 0; $i < $form_state['values']['num_compliance']; $i++){
    if ($form_state['values']['row-' . $i]['route'] == 1){
      // Add admin_route to compliance
      $node = node_load($form_state['values']['row-' . $i]['nid']);
      $node->field_compliance_admin_route[$node->language][] = array('value' => $form_state['values']['routee']);
      if ($node = node_submit($node)) { // Prepare node for saving
        node_save($node);
      }
      $routed_nodes[] = $node;
    }
  }

  // Send email collating all checked pms
  // Get admin active setting boolean
  if (variable_get('route_email', 1)){
    $message = decode_entities(t('@message', array('@message' => variable_get('route_message', 'A researcher/scholar needs your help complying with one or more protection measures in the researcher/scholar\'s new submission.'))));
    $research_data_node = node_load($routed_nodes[0]->field_compliance_data[$routed_nodes[0]->language][0]['nid']);
    $submitter = user_load($research_data_node->uid);
    if (empty($research_data_node->field_research_affiliation_ref[$research_data_node->language][0]['tid'])) {
      $affiliation = $research_data_node->field_research_affiliation_other[$research_data_node->language][0]['value'];
    }
    else {
      $affiliation = taxonomy_term_load($research_data_node->field_research_affiliation_ref[$research_data_node->language][0]['tid']);
      $affiliation = $affiliation->name;
    }
    $data_types = '';
    $dts = $research_data_node->field_research_data_type_ref[$research_data_node->language];
    $dts_size = count($dts);
    for ($i = 0; $i < $dts_size; $i++){
      $dt_node = node_load($dts[$i]['nid']);
      $data_types .= $dt_node->title;
      // Format array to sentence structure
      if ($dts_size == 2 && ($dts_size - 1) > $i) {
        $data_types .= ' and ';
      }
      elseif ($dts_size > 2 && ($dts_size - 2) > $i) {
        $data_types .= ', ';
      }
      elseif ($dts_size > 2 && ($dts_size - 1) > $i) {
        $data_types .= ', and ';
      }
      else {
        // $data_types .= '.';
      }
    }

    $replacements = array(
      '@field_of_research' => '<b>' . $research_data_node->title . '</b>',
      '@submitter' => '<b>' . $submitter->name . '</b>',
      '@sensitivity' => '<b>' . $research_data_node->field_research_sensitivity[$research_data_node->language][0]['value'] . '</b>',
      '@principal_investigator' => '<b>' . $research_data_node->field_research_pi[$research_data_node->language][0]['value'] . '</b>',
      '@affiliation' => '<b>' . $affiliation . '</b>',
      '@key_admin' => '<b>' . $research_data_node->field_research_key_admin[$research_data_node->language][0]['value'] . '</b>',
      '@research_focus' => $research_data_node->body[$research_data_node->language][0]['value'],
      '@data_types' => '<b>' . $data_types . '</b>',
    );

    $message = format_string($message, $replacements);

    // $message .= '<br /><br />';
    $message .= "\n\n" . '<p>' . t('@pi needs help complying with the following protection measures:', array('@pi' => $research_data_node->field_research_pi[$research_data_node->language][0]['value'])) . "\n\n";
    foreach ($routed_nodes as $routed_node) {
      $pm_node = node_load($routed_node->field_compliance_pm[$routed_node->language][0]['nid']);
      $message .= '- ' . $pm_node->title . "\n";
    }
    $message .= '</p>' . "\n\n";

    $message .= '<p>' . t('Once compliant with all these protection measures, please return to this Research and Scholarship Data profile to confirm it is complete:') . '</p>';

    $path_to_confirmation = 'admin/data/' . $research_data_node->nid . '/route/' . check_url($form_state['values']['routee']) . '/confirm';
    $message .= '<p>' . l($base_url . $path_to_confirmation, $path_to_confirmation) . '</p>';

    watchdog('lsadataclassify', 'message before: !notification', array('!notification' => $message), WATCHDOG_NOTICE);
    $message = drupal_html_to_text($message);
    watchdog('lsadataclassify', 'message after: !notification', array('!notification' => $message), WATCHDOG_NOTICE);

    lsadataclassify_mail_send(array('email' => $form_state['values']['routee'] . '@umich.edu', 'message' => $message));
  }

}

function lsadataclassify_mail_send($form_values) {
  // All system mails need to specify the module and template key (mirrored from
  // hook_mail()) that the message they want to send comes from.
  $module = 'lsadataclassify';
  $key = 'contact_message';

  // Specify 'to' and 'from' addresses.
  $to = $form_values['email'];
  $from = variable_get('site_mail', 'admin@example.com');

  // "params" loads in additional context for email content completion in
  // hook_mail(). In this case, we want to pass in the values the user entered
  // into the form, which include the message body in $form_values['message'].
  $params = $form_values;

  // The language of the e-mail. This will one of three values:
  // * user_preferred_language(): Used for sending mail to a particular website
//   user, so that the mail appears in their preferred language.
  // * global $language: Used when sending a mail back to the user currently
//   viewing the site. This will send it in the language they're currently
//   using.
  // * language_default(): Used when sending mail to a pre-existing, 'neutral'
//   address, such as the system e-mail address, or when you're unsure of the
//   language preferences of the intended recipient.
  //
  // Since in our case, we are sending a message to a random e-mail address that
  // is not necessarily tied to a user account, we will use the site's default
  // language.
  $language = language_default();

  // Whether or not to automatically send the mail when drupal_mail() is
  // called. This defaults to TRUE, and is normally what you want unless you
  // need to do additional processing before drupal_mail_send() is called.
  $send = TRUE;
  // Send the mail, and check for success. Note that this does not guarantee
  // message delivery; only that there were no PHP-related issues encountered
  // while sending.
  $result = drupal_mail($module, $key, $to, $language, $params, $from, $send);
  if ($result['result'] == TRUE) {
    drupal_set_message(t('These protection measures have been routed and an email has been sent.'));
  }
  else {
    drupal_set_message(t('There was a problem routing these protection measures and the email was not sent.'), 'error');
  }

}