I'm unable to create a PDF from an entire web site ... this option once worked, but it now only creates a blank pdf with the url and timestamp. Has there been any changes to this feature? Are there any other ways to do so? I've tried by going File > Create > PDF from Web Page ... and I've also tried using the plugin on my web browser (but this only allows for a single page and not entire site.)
If you're trying to do that you need to verify the domain levels of that website. Sometimes there are areas in those websites that are restricted from access or only grant privileged access to certain users with a user account and password.
The first method that you tried lets you specify with a number the domain levels. There is an option for that when using the Create PDF from Website wizard.