ConnorK [ConnorK]

    $block['subject'] = variable_get('adjustisearch_block_title', 'Search:');

Verry minor, but you should do 'Search:' translateable.

adjustisearch_form_builder

Thats just a comment, you don't use any lines together with the two different formIds. Why not just use two form functions for the two forms.
Then you could save hook_forms.

1. Use the Drupal string functions when available.

2.   $form_state['values']['adjustisearch_block_title'] = check_plain($form_state['values']['adjustisearch_block_title']);
     $form_state['values']['adjustisearch_url_list'] = check_plain($form_state['values']['adjustisearch_url_list']);
     $form_state['values']['adjustisearch_box_size'] = check_plain($form_state['values']['adjustisearch_box_size']);
   

   A validate function should only validate the data, not modify it. Then, the data are filtered in output, not in input; differently, users would see & altered in &, when they change the settings for the second time.

    '#description'   => t("Enter the URL search list, with one URL per line. These URLs must be entered in <i>Adjusti-Search URL Format (ASUF)</i>, which can be found on the <a href='../help/adjustisearch' target='_blank'>Adjusti-Search help page</a>. Any URL not in <i>ASUF</i> will be ignored."),

I am not sure the relative URL would work; what should it point to (../help/adjustisearch)?

The rest is fine.