I've just gotten a site I'm supposed to do some work on but I'm having trouble with migrating to a local development environment. I don't have admin access to the site itself, but I do have access to the server. I pulled the database down along with the code base, but I seem to have messed up the file permissions when moving the site because the site loads, but not all the functionality is present.

The site isn't accessible beyond the splash page, and none of the image assets load except the site logo. Accessing any menu links generates a 404. The image that loads has the same ownership and permissions as the image which loads which are myuser:www-data and 640. Initially, no images loaded, but following this post about securing file permissions got the logo loaded.

I am also having issues with accessing the site. Since, I can't access any menus beyond the root, it seems that I can't access the login page either. I've added a user for myself with Drush, and even run drush uli with the the URI provided as a parameter, but the link is inaccessible and returns a 404. I also used the File Permissions module, but it doesn't seem to have helped.

At this point, my next step is going to be setting up a clean install and importing the db through backup and migrate and moving the theme and modules manually, but I'd like to figure out what I did wrong and how to avoid this.