Updating node field value using custom module validation
I worked out that I was using

   $form['actions']['submit']['#submit'][] = 'sitefuncs_custom_submit';


When it should have been

   $form['actions']['submit']['#validate'][] = 'sitefuncs_custom_submit';


Then all my data saved using 

$form_state['values']['field_stage_complete_text']['und'][0]['value']['#value'] = 'No'; // set value to No