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.
The letter of the copyright law is extremely weird in such cases (formally you may need to request a permission from the journal editor to reproduce something, especially a picture, you made and submitted there yourself a few years ago, if you have assigned copyrights-some journals require copyright transfer, some do not). However, the spirit of the law is that you are free to use your own work several times even if you assigned your copyright away as long as you clearly state that it is not the first time you present (this is not required if you both retain all the rights and no originality expected) it and that the previous publications are such and such. To be on the safe side, write to the editors and request a permission to reprint (it is automatic unless the editor is an evil villain having personal grudge against you). However anyone trying to accuse you of using your own work without his permission will make such a fool of himself in the scientific world that his reputation there will plummet to negative infinity, so I don't think the chances of trouble are above those that some crank will accuse you of plagiarizing his work or that the outcome of the accusation, if it occurs, will be essentially different.
The papers you have published and that my be under review in a journal require permission to rproduce. It is therefore necessary to write to the journals and ask for permission to reproduce the contents in a thesis. I have heard of journals that refuse but they are very few. What you should remember, however, is that the copyright usually covers the final product or versions of the manuscript that have been altered as a result of work done within the journal, in other words gone through or in some stage of review. It would therefore be safe to reproduce your original submitted manuscript. You will need to acknowledge the permissions in your thesis (e.g. if you include a list of published paers and manuscripts in prep.).
All this may seem complicated but I have not experienced any publisher that has refused reproduction (either of a reprint or the text itself) in a thesis. After all, publishers live off of scientists writing papers and a PhD candidate (and scientists involved with her/him) is another "customer" to put it bluntly. It would therefore potentially be pretty self-destructive to refuse use of materials for a thesis with very limited distrubution.
Under any circumstances, please contact publishersand tell them what you intend to do andaskfor permission. Also check on the copyrights (which you usually sign at some point during the publication process. It is "better safe that sorry" that applies. And, I repeat, I would be surprised if you are given a no.
EDIT: A good way to find out what "your" journal adheres to is ot use the SHERPA/RoMEO site classification for self-archiving. They use a four part classification as follows:
green - can archive pre-print and post-print or publisher's version/PDF
blue - can archive post-print (i.e. final draft post-refereeing) or publisher's version/PDF
yellow - can archive pre-print (i.e. pre-refereeing)
white - archiving not formally supported
The level or archiving indcates what also falls under the copyright agreement of each journal and hence also what you may be free to reproduce in a thesis, and what you are not.