You have several extra files in -/includes/modules/shipping/ which you need to delete from your server:

flat.php
freeoptions.php
freeshipper.php
html_header.php
item.php
perweightunit.php
shopping_cart.php
storepickup.php
stylesheet.css
stylesheet_new.css
table.php
tpl_account_edit_default.php
tpl_account_history_info_default.php
tpl_main_page.php
tpl_search.php
tpl_search_header.php
tpl_shopping_cart.php
tpl_tabular_display.php
ups.php
usps.php
zones.php