Self-Plagiarism in PhD thesis
Even if your department does not allow a "stapler" thesis, it is entirely reasonable to expect that you should be able to freely use this material in a thesis. In general, I would expect that you would have to include a copyright statement similar in form to hose that would be used were you to copy the entire paper outright.

To cover against charges of plagiarism, I would simply acknowledge something like "Some passages have been quoted verbatim from the following sources," and list them. Also, when you reuse figures, I'd include the "reprinted with permission" tag. 

Finally, ask your advisor or other members of your department for guidance! Since you're not the only person subject to this restriction, they've gone through this situation before, and can provide you with information on how former students have handled this.