EDIT: Fixed.
I had to go and find all four config files and update them with the core path. This is mentioned nowhere in the MODX instructions and I came across it by chance after looking at 20 posts and finally seeing the comment by the famous Bobby Ray. Thanks Bob!
define('MODX_CORE_PATH', dirname(__FILE__) . '/core/'); define('MODX_CONFIG_KEY', 'config');
@Anton, do you know if UpgradeMODX will still work with relative paths in the config.core.php files?