"I recommend you nofollow the login, search, and cart pages through XML layout. That will cross off another 500 pages or so." Not nofollow. Don't use nofollow . This is for untrusted links - so should not be used for internal links.
It's Noindex. And then use the canonical tag if 301 Redirects are not an option. To make life more complicated, you need to be careful not to do use noindex and canonical tag simultaneously.
