The login and registration where working for me when i tested.
the issue with the cart page directing to the checkout page was due to spaces between php code blocks, i removed those to fix the problem.
the other issues are caused by adding your template to all of the checkout pages.
the confirm_cart and confirm pages should not have your template applied to them. those pages are loaded into the checkout page via ajax, they will not be accessed directly so should not have the template applied. apply the template to the checkout page only.