diff --git modules/panels.skinr.inc modules/panels.skinr.inc
index 01f633e..7e60bed 100644
--- modules/panels.skinr.inc
+++ modules/panels.skinr.inc
@@ -22,6 +22,9 @@ function panels_skinr_config_info() {
   $data['panels']['preprocess']['panels_pane'] = array(
     'index_handler' => 'panels_skinr_preprocess_index_handler',
   );
+  $data['panels']['contextual_links']['panels_pane'] = array(
+    'contextual_links_handler' => 'panels_skinr_contextual_links',
+  );
 
   return $data;
 }
@@ -67,20 +70,26 @@ function panels_skinr_preprocess_index_handler(&$variables) {
 }
 
 /**
- * Implements hook_panels_pane_content_alter().
+ * Skinr contextual links handler.
+ *
+ * @param &$variables
+ *   Passes in the $variables parameter from skinr_preprocess().
  *
- * Because of the way panels handles contextual links we can't use a
- * contextual links handler.
+ * @return
+ *   An array. Each value is an array that forms the function arguments for
+ *   menu_contextual_links(). For example:
+ *   @code
+ *     array(
+ *       'admin/appearance/skinr/edit', array('system', 'navigation')),
+ *     )
+ *   @endcode
  */
-function panels_panels_pane_content_alter(&$content, $pane, $display_args, $context) {
-  if (user_access('edit skin settings')) {
-    $element = 'pane__' . $pane->did . '__' . $pane->pid;
-    $content->admin_links[] = array(
-      'title' => t('Edit skin'),
-      'href' => 'admin/appearance/skinr/edit/nojs/panels/' . $element . '/configure',
-      'query' => drupal_get_destination(),
-    );
-  }
+function panels_skinr_contextual_links(&$variables) {
+  $links = array();
+  $links['skinr-panels'] = array(
+    'admin/appearance/skinr/edit/nojs', array('panels', 'pane__' . $variables['pane']->did . '__' . $variables['pane']->pid),
+  );
+  return $links;
 }
 
 /**
diff --git skinr.module skinr.module
index 8b6a3e3..597fb51 100644
--- skinr.module
+++ skinr.module
@@ -62,28 +62,6 @@ function skinr_cache_reset() {
 }
 
 /**
- * Implements hook_module_implements_alter().
- */
-function skinr_module_implements_alter(&$implementations, $hook) {
-  // Run Skinr first to avoid issues with other modules during hook_init().
-  if ($hook == 'init') {
-    $skinr['skinr'] = $implementations['skinr'];
-    unset($implementations['skinr']);
-    $implementations = array_merge($skinr, $implementations);
-  }
-}
-
-/**
- * Implements hook_init().
- *
- * @todo Kill me. Entirely.
- */
-function skinr_init() {
-  module_load_include('inc', 'skinr', 'skinr.handlers');
-  skinr_load_includes();
-}
-
-/**
  * Implements hook_preprocess().
  *
  * @todo Optimize this function by removing dependencies on
@@ -444,6 +422,11 @@ function skinr_implements() {
 
   if (!isset($cache)) {
     $cache = array();
+
+    // Load built-in support code for Drupal core modules.
+    // @todo Remove this when we eliminate skinr handlers.
+    module_load_include('inc', 'skinr', 'skinr.handlers');
+
     // Collect hook_skinr_api_VERSION() module implementations. This will also
     // auto-load $module.skinr.inc files, which may contain skin/group hook
     // implementations (when not using the plugin system).
@@ -465,9 +448,14 @@ function skinr_implements() {
       // $module.skinr.inc file and auto-load it. module_implements() only
       // auto-loads $module.skinr.inc in a module's root folder.
       if (isset($cache[$module]['path'])) {
-        $file = DRUPAL_ROOT . '/' . $cache[$module]['path'] . '/' . $module . '.skinr.inc';
-        if (file_exists($file)) {
-          require_once $file;
+        $file = $cache[$module]['path'] . '/' . $module . '.skinr.inc';
+        if (file_exists(DRUPAL_ROOT . '/' . $file)) {
+          $cache[$module]['include file'] = $file;
+          // When rebuilding the cache, we auto-load the include file for
+          // convenience. Calling code should invoke skinr_load_includes()
+          // on the extensions they want to act with.
+          // @todo Remove this.
+          include_once DRUPAL_ROOT . '/' . $file;
         }
       }
       // Populate defaults.
@@ -537,9 +525,14 @@ function skinr_implements() {
         );
         // Lastly, for API consistency with modules, check whether the theme
         // contains a $theme.skinr.inc file and auto-load it, if any.
-        $file = DRUPAL_ROOT . '/' . $cache[$name]['path'] . '/' . $name . '.skinr.inc';
-        if (file_exists($file)) {
-          require_once $file;
+        $file = $cache[$name]['path'] . '/' . $name . '.skinr.inc';
+        if (file_exists(DRUPAL_ROOT . '/' . $file)) {
+          $cache[$name]['include file'] = $file;
+          // When rebuilding the cache, we auto-load the include file for
+          // convenience. Calling code should invoke skinr_load_includes()
+          // on the extensions they want to act with.
+          // @todo Remove this.
+          include_once DRUPAL_ROOT . '/' . $file;
         }
       }
     }
@@ -549,15 +542,15 @@ function skinr_implements() {
 }
 
 /**
- * Includes $extension.skinr.inc files of extensions compatible with this version of Skinr.
+ * Loads $extension.skinr.inc include files of passed in extensions.
  *
- * @todo Shoot me. Twice.
+ * @todo These hook implementations should not be required to be loaded at all,
+ *   rewrite the code that is currently not using the cache.
  */
-function skinr_load_includes() {
-  foreach (skinr_implements() as $extension) {
-    $file = DRUPAL_ROOT . '/' . $extension['path'] . '/' . $extension['name'] . '.skinr.inc';
-    if (file_exists($file)) {
-      require_once $file;
+function skinr_load_includes(array $extensions) {
+  foreach ($extensions as $extension) {
+    if (isset($extension['include file'])) {
+      include_once DRUPAL_ROOT . '/' . $extension['include file'];
     }
   }
 }
@@ -1206,6 +1199,11 @@ function skinr_get_config_info() {
   if (!isset($config_info)) {
     if ($cached = cache_get('skinr_config_info')) {
       $config_info = $cached->data;
+
+      // Load the module integration files.
+      // @todo Whatever currently needs to be invoked has to be cached instead.
+      skinr_load_includes($config_info);
+
       return $config_info;
     }
     $config_info = array();
@@ -1215,6 +1213,13 @@ function skinr_get_config_info() {
       if (function_exists($function)) {
         $extension_info = $function();
         if (isset($extension_info) && is_array($extension_info)) {
+          // @todo Yuck! Rewrite hook_skinr_config_info() API structure. Why do
+          //   implementations return info keyed by their own module name?
+          if (isset($extension['include file'])) {
+            foreach ($extension_info as &$info) {
+              $info['include file'] = $extension['include file'];
+            }
+          }
           $config_info = array_merge_recursive($config_info, $extension_info);
         }
       }
@@ -1314,6 +1319,12 @@ function skinr_config_info_default() {
  * @param $a7
  */
 function skinr_handler($type, $op, $handler, &$a3, $a4 = NULL, $a5 = NULL, $a6 = NULL, $a7 = NULL) {
+  // @todo Once we eliminate skinr_handler, all functions in skinr.handlers.inc can
+  //   be moved out of it and the file eliminated.
+  if (in_array($handler, array('skinr_access_handler', 'skinr_index_handler', 'skinr_data_handler', 'skinr_submit_handler'))) {
+    module_load_include('inc', 'skinr', 'skinr.handlers');
+  }
+
   if (is_callable($handler)) {
     switch ($type) {
       case 'contextual_links':
diff --git skinr_ui.module skinr_ui.module
index bbc9e61..947d6c9 100644
--- skinr_ui.module
+++ skinr_ui.module
@@ -6,6 +6,31 @@
  */
 
 /**
+ * Implements hook_theme_registry_alter().
+ *
+ * Re-order preprocess functions to prioritize skinr_ui_preprocess, which adds
+ * contextual links, over template_preprocess_HOOK functions. This fixes a
+ * problem with the way panels handles contextual links.
+ */
+function skinr_ui_theme_registry_alter(&$theme_registry) {
+  $preprocess_functions = array();
+  foreach ($theme_registry['panels_pane']['preprocess functions'] as $function) {
+    if ($function == 'skinr_ui_preprocess') {
+      continue;
+    }
+
+    $preprocess_functions[] = $function;
+
+    if ($function == 'template_preprocess') {
+      // Insert our preprocess function right after template_preprocess to give it priority over template_preprocess_HOOK functions.
+      $preprocess_functions[] = 'skinr_ui_preprocess';
+    }
+  }
+
+  $theme_registry['panels_pane']['preprocess functions'] = $preprocess_functions;
+}
+
+/**
  * Implements hook_permission().
  */
 function skinr_ui_permission() {
@@ -668,6 +693,10 @@ function skinr_ui_preprocess(&$variables, $hook) {
       }
     }
   }
+  if ($hook == 'panels_pane') {
+    dpm('skinr_ui_preprocess [' . $original_hook . ']');
+    dpm($variables['content']->content);
+  }
 }
 
 /**
@@ -687,15 +716,19 @@ function skinr_ui_contextual_links(&$variables, $hook, $contextual_links) {
   $hooks = theme_get_registry();
 
   // Determine the primary theme function argument.
-  if (isset($hooks[$hook]['variables'])) {
+  if (!empty($hooks[$hook]['variables'])) {
     $keys = array_keys($hooks[$hook]['variables']);
     $key = $keys[0];
   }
-  else {
+  elseif (!empty($hooks[$hook]['render element'])) {
     $key = $hooks[$hook]['render element'];
   }
-  if (isset($variables[$key])) {
-    $element =& $variables[$key];
+  if ($hook == 'panels_pane') {
+    // Exception for panels_pane.
+    $element = &$variables['content']->content;
+  }
+  elseif (!empty($key) && isset($variables[$key])) {
+    $element = &$variables[$key];
   }
 
   if (isset($element) && is_array($element)) {
diff --git tests/skinr.test tests/skinr.test
index 2d6ee92..1b78578 100644
--- tests/skinr.test
+++ tests/skinr.test
@@ -5,6 +5,46 @@
  * Tests for the Skinr module.
  */
 
+class SkinrWebTestCase extends DrupalWebTestCase {
+  /**
+   * Asserts that a class is set for the given element id.
+   *
+   * @param $id
+   *   Id of the HTML element to check.
+   * @param $class
+   *   The class name to check for.
+   * @param $message
+   *   Message to display.
+   * @return
+   *   TRUE on pass, FALSE on fail.
+   */
+  function assertSkinrClass($id, $class, $message = '') {
+    $elements = $this->xpath('//div[@id=:id and contains(@class, :class)]', array(
+      ':id' => $id,
+      ':class' => $class,
+    ));
+    $this->assertTrue(!empty($elements[0]), $message);
+  }
+
+  /**
+   * Asserts that a class is not set for the given element id.
+   *
+   * @param $id
+   *   Id of the HTML element to check.
+   * @param $class
+   *   The class name to check for.
+   * @param $message
+   *   Message to display.
+   * @return
+   *   TRUE on pass, FALSE on fail.
+   */
+  function assertNoSkinrClass($id, $class, $message = '') {
+    $elements = $this->xpath('//div[@id=:id]', array(':id' => $id));
+    $class_attr = (string) $elements[0]['class'];
+    $this->assertTrue(strpos($class_attr, $class) === FALSE, $message);
+  }
+}
+
 /**
  * Tests basic module installation.
  */
@@ -86,7 +126,7 @@ class SkinrInstallationTestCase extends DrupalWebTestCase {
  *
  * @link http://drupal.org/node/953336#comment-3738456 Make sure this patch is applied to drupal core @endlink
  */
-class SkinrApiTestCase extends DrupalWebTestCase {
+class SkinrApiTestCase extends SkinrWebTestCase {
   protected $profile = 'testing';
 
   public static function getInfo() {
@@ -140,6 +180,7 @@ class SkinrApiTestCase extends DrupalWebTestCase {
       'node' => array(
         'version' => VERSION,
         'path' => drupal_get_path('module', 'skinr') . '/modules',
+        'include file' => drupal_get_path('module', 'skinr') . '/modules/node.skinr.inc',
       ),
       // skinr_test has been installed.
       'skinr_test' => array(
@@ -151,6 +192,7 @@ class SkinrApiTestCase extends DrupalWebTestCase {
         'directory' => 'skins',
         'base themes' => array(),
         'sub themes' => drupal_map_assoc(array('skinr_test_subtheme')),
+        'include file' => drupal_get_path('theme', 'skinr_test_basetheme') . '/skinr_test_basetheme.skinr.inc',
       ),
       'skinr_test_subtheme' => array(
         'type' => 'theme',
@@ -158,6 +200,7 @@ class SkinrApiTestCase extends DrupalWebTestCase {
         'directory' => 'skins',
         'base themes' => drupal_map_assoc(array('skinr_test_basetheme')),
         'sub themes' => array(),
+        'include file' => drupal_get_path('theme', 'skinr_test_subtheme') . '/skinr_test_subtheme.skinr.inc',
       ),
     );
     // When running tests on Skinr code packaged by drupal.org, all 'version'
@@ -189,6 +232,61 @@ class SkinrApiTestCase extends DrupalWebTestCase {
   }
 
   /**
+   * Tests skinr_implements() caching and auto-loading.
+   */
+  function testSkinrImplementsCache() {
+    module_enable(array('block'));
+    // Enable main system block for content region and the user menu block for
+    // the first sidebar.
+    $default_theme = variable_get('theme_default', 'bartik');
+    db_merge('block')
+      ->key(array(
+        'theme' => $default_theme,
+        'module' => 'system',
+        'delta' => 'main',
+      ))
+      ->fields(array(
+        'status' => 1,
+        'region' => 'content',
+        'pages' => '',
+      ))
+      ->execute();
+    db_merge('block')
+      ->key(array(
+        'theme' => $default_theme,
+        'module' => 'system',
+        'delta' => 'powered-by',
+      ))
+      ->fields(array(
+        'status' => 1,
+        'region' => 'sidebar_first',
+        'pages' => '',
+      ))
+      ->execute();
+
+    // Enable a skin defined in an include file, which applies to a module
+    // element that is equally registered in an include file (built-in Block
+    // module integration).
+    $skin = (object) array(
+      'theme' => $default_theme,
+      'module' => 'block',
+      'element' => 'system__powered-by',
+      'skin' => 'skinr_test_font',
+      'options' => array('font_1'),
+      'status' => 1,
+    );
+    skinr_skin_save($skin);
+
+    // Verify the skin is contained in the output.
+    $this->drupalGet('');
+    $this->assertSkinrClass('block-system-powered-by', 'font-1', 'Skin found.');
+
+    // Once again, so we hit the cache.
+    $this->drupalGet('');
+    $this->assertSkinrClass('block-system-powered-by', 'font-1', 'Skin found.');
+  }
+
+  /**
    * Tests hook_skinr_skin_info().
    */
   public function testSkinrSkinInfo() {
@@ -422,7 +520,7 @@ class SkinrApiTestCase extends DrupalWebTestCase {
  *
  * @link http://drupal.org/node/953336#comment-3738456 Make sure this patch is applied to drupal core @endlink
  */
-class SkinrDisplayTestCase extends DrupalWebTestCase {
+class SkinrDisplayTestCase extends SkinrWebTestCase {
   protected $profile = 'testing';
 
   public static function getInfo() {
@@ -474,42 +572,6 @@ class SkinrDisplayTestCase extends DrupalWebTestCase {
     theme_enable(array('garland'));
   }
 
-  /**
-   * Asserts that a class is set for the given element id.
-   *
-   * @param $id
-   *   Id of the HTML element to check.
-   * @param $class
-   *   The class name to check for.
-   * @param $message
-   *   Message to display.
-   * @return
-   *   TRUE on pass, FALSE on fail.
-   */
-  function assertSkinrClass($id, $class, $message = '') {
-    $elements = $this->xpath('//div[@id=:id]', array(':id' => $id));
-    $class_attr = (string) $elements[0]['class'];
-    $this->assertTrue(strpos($class_attr, ' ' . $class . ' '), $message);
-  }
-
-  /**
-   * Asserts that a class is not set for the given element id.
-   *
-   * @param $id
-   *   Id of the HTML element to check.
-   * @param $class
-   *   The class name to check for.
-   * @param $message
-   *   Message to display.
-   * @return
-   *   TRUE on pass, FALSE on fail.
-   */
-  function assertNoSkinrClass($id, $class, $message = '') {
-    $elements = $this->xpath('//div[@id=:id]', array(':id' => $id));
-    $class_attr = (string) $elements[0]['class'];
-    $this->assertFalse(strpos($class_attr, ' ' . $class . ' '), $message);
-  }
-
   public function testSkinrDisplayed() {
     // Save a skin configuration object.
     $skin = (object) array(