Are there general guidelines for order of front and back matter sections in a thesis?
One of the wonderful things about your thesis is that it is one of the few documents that there is very little constraint on how you are allowed to arrange it.  Once you have satisfied the university's formal requirements (of which there are often few), it is up to you (with, of course, the consent of your advisor).  So arrange things however you feel makes the most clear and accessible presentation, and it will be OK.