Thanks for that fix gruant2000381341.
Just changing the first two lines you mention does it:
$Config['UserFilesPath'] = 'http://'.$_SERVER['HTTP_HOST'].'/FCKeditor/uploadfiles/' ;
$Config['UserFilesAbsolutePath'] = $_SERVER['DOCUMENT_ROOT'].'/FCKeditor/uploadfiles/' ;
The lines below it don't need to change but you also need to make sure that your remote root is defined correctly, as nothing in the line above those two (around line 27):
$WA_EditorRemoteRoot = '';