There are two changes that need to be made. The first of them simple:
webform.submissions
include_once(drupal_get_path('module', 'webform') .'/webform_submissions.inc');
module_load_include('inc', 'webform', 'includes/webform.submissions');
hook_form_alter()
for modifying the form$form_values
, but now use $form_state['values']
$form_state['values']['submitted_tree']['facility'] = $facilityid_name; //email $form_state['values']['submitted'][23] = $facilityid_id; // database