How to add "#main-content" to the link of pager element?
You can use template_preprocess_pager to alter the pager links. You should be able to do something like the following for whatever links within the pager you want to change:

function MYTHEME_preprocess_pager(&amp;$variables) {
  if (some check to make sure its the pager you want){ 
    $cur = $variables['items']['next']['href'];
    $variables['items']['next']['href'] =  $cur . '#main-content';
  }
}