Print module PDF attachment
It seems it was a silly mistake on my behalf.  

My module defined a custom path to send the email and the theme files for the pdf were in the admin theme folder, so I had to set my path to use the admin theme for the email theme files to be found.
I did so by implementing HOOK_custom_theme.

function custom_send_email_custom_theme() {
  return variable_get('admin_theme');
} 


I will leave this question up as the code may help someone in the future (and maybe me if I need to send an email with attachments again :) )