Unfortunately Scribus currently - as of 1.4.3 - can't do number variables or cross references. There are some fudges that work in some cases but they're nasty and should be avoided, in my opinion. Scribus can do simple TOCs but the functionality is limited.
However, and here's the good news - if you can wait - there are some very good additions coming to Scribus in version 1.5. These include variables, footnotes, and other reference functions. I don't know if there are any TOC improvements.
The last time I looked at 1.5.0svn - the "beta" of the next version - these features were coming on quite well - apart from various UI issues which will probably be sorted before the production version. (Unfortunately my copy of 1.5.0svn doesn't load anymore so I can't give you more details, but that's probably because of something I upgraded/changed and not a problem with Scribus itself.)
I've no idea if there are any 1.5.0svn installation builds available but if you are okay compiling your own code you can download the source and take it from there.
I also have no idea when 1.5 will be available as the stable version but the wait might be worth it. Maybe another forum member has more inside info?
It's worth noting that if you get a 1.5.0svn installation it will probably work fine but be aware that documents saved by it might not load in future releases if they use features that are discontinued or changed. And 1.4.3 can't load 1.5.0 documents either so you can't revert back to the last stable version. But it might be worth having a look anyway to see if it will do what you want when it comes out.
Having said all of that, lots of people have created long/complex publications using Scribus so you could have a look at the Success Stories section of the Wiki for some inspiration. See
http://wiki.scribus.net/canvas/Success_stories_2013 and the links on the right of that page for more.
P.S. Your book looks great by the way.