diff --git a/src/BaseCommand.php b/src/BaseCommand.php
index d2312d0..74631c3 100644
--- a/src/BaseCommand.php
+++ b/src/BaseCommand.php
@@ -26,6 +26,7 @@ abstract class BaseCommand extends Command
 
     public $loadConfig = true;
     public $loadMODX = true;
+    public $isUpgrade = false;
 
     /**
      * Initializes the command just after the input has been validated.
diff --git a/src/Command/UpgradeModxCommand.php b/src/Command/UpgradeModxCommand.php
index 69c7eae..186ac33 100644
--- a/src/Command/UpgradeModxCommand.php
+++ b/src/Command/UpgradeModxCommand.php
@@ -19,6 +19,7 @@ class UpgradeModxCommand extends BaseCommand
 
     public $loadConfig = false;
     public $loadModx = true;
+    public $isUpgrade = true;
 
     protected function configure()
     {
@@ -58,13 +59,17 @@ protected function execute(InputInterface $input, OutputInterface $output)
 
         // Actually run the CLI setup
         exec("php -d date.timezone={$tz} {$wd}setup/index.php --installmode=upgrade --config={$config}", $setupOutput);
-        $output->writeln($setupOutput[0]);
 
         // Try to clean up the config file
         if (!unlink($config)) {
             $output->writeln("<warning>Warning:: could not clean up the setup config file, please remove this manually.</warning>");
         }
 
+        // Remove setup directory if upgrade process left it there.
+        if (is_dir("{$wd}setup/")) {
+            exec("rm -rf {$wd}setup/");
+        }
+
         $output->writeln('Done! ' . $this->getRunStats());
 
         return 0;
diff --git a/src/Mixins/DownloadModx.php b/src/Mixins/DownloadModx.php
index 05df46a..fce4c19 100644
--- a/src/Mixins/DownloadModx.php
+++ b/src/Mixins/DownloadModx.php
@@ -73,6 +73,7 @@ protected function download($version)
      * Unzips the package zip to the current directory
      *
      * @param $package
+     * @throws \Exception
      */
     protected function unzip($package)
     {
@@ -108,7 +109,7 @@ protected function fetchUrl($version)
         $ch = curl_init();
         curl_setopt($ch, CURLOPT_URL, $url);
         curl_setopt($ch, CURLOPT_CONNECTTIMEOUT, 0);
-        curl_setopt($ch, CURLOPT_TIMEOUT, 10);
+        curl_setopt($ch, CURLOPT_TIMEOUT, 30);
         curl_setopt($ch, CURLOPT_FOLLOWLOCATION, 1);
         curl_setopt($ch, CURLOPT_NOBODY, 1);
         curl_exec($ch);
@@ -131,14 +132,50 @@ protected function retrieveFromCache($version)
     {
         $version = 'modx-' . str_replace('modx-', '', $version);
 
-
         $path = GITIFY_CACHE_DIR . $version;
 
         if (!file_exists($path) || !is_dir($path)) {
             $this->download($version);
         }
 
-        exec("cp -r $path/* ./");
+        // Handle potential custom paths on upgrade
+        if ($this->isUpgrade) {
+            require_once './config.core.php';
+            if (MODX_CORE_PATH) {
+                require_once MODX_CORE_PATH . 'config/config.inc.php';
+                // Need to avoid the easier route with rsync as it may not be installed
+                $paths = [
+                    'core' => MODX_CORE_PATH,
+                    'connectors' => MODX_CONNECTORS_PATH,
+                    'manager' => MODX_MANAGER_PATH
+                ];
+                foreach ($paths as $k => $customPath) {
+                    // Throw out default config files
+                    if (file_exists("$path/$k/config.core.php")) {
+                        unlink("$path/$k/config.core.php");
+                    }
+                    // Copy each dir to path specified in config file then remove that dir from source
+                    exec("cp -r $path/$k/* $customPath");
+                    exec("rm -rf $path/$k");
+                }
+
+                unlink("$path/config.core.php");
+
+                // Now copy remaining contents
+                exec("cp -r $path/* ./");
+
+                // Hard wipe cache
+                if (is_dir(MODX_CORE_PATH . 'cache/')) {
+                    exec('rm -rf ' . MODX_CORE_PATH . 'cache/*');
+                }
+
+                // Re-extract package to source dir, so it's ready for another run.
+                $this->unzip($path . '.zip');
+            }
+        }
+        else {
+            exec("cp -r $path/* ./");
+        }
     }
 
     /**