It seems you've set the "Relative path to the Contao directory" setting to something like "www.domain.com/website". I think it would need to be either of: '/website' or '' (empty).
If I set it to the wrong value my backend won't work and I can't fix it (perhaps the install tool can (install.php)). However, if this is the case try editing your /system/config/localconfig.php file. Look for the following setting and try one of the earlier mentioned settings.
Code:
$GLOBALS['TL_CONFIG']['websitePath'] = '';
Also, you mentioned you've made some changes to templates files? You will have to undo those as well..
ps, I'm assuming you've installed contao in a subfolder called "website" on your server rather then the http-root. If your website is inside the root then the mentioned setting must certainly be left empty, otherwise it must contain the relative path starting from the root, eg; "website"
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