Okay I got your Categories back; I had to do a forum reset (this means you lost any category edits, or if the categories were in books, they need to be added again). Books was harder, I had to run a few queries. I think maybe there is a bug in the importer for books, but this is very hard to debug.
Books did not contain any text to edit because the import added comment tags, and there is a bug in the converter that removes COMMENT, NOPARSE, CODE, HTML, and PHP tags.
I restored the missing Header content, but your last-edited user will be unlinkable until a new edit is made.
It looks like the NuWiki importer doesn't format existing wiki articles. It assumes this was handled in a DM, which it appears it was not. The result is that the articles disappear on the next URL build.