Specifically, I'd like to be able to show a TOC and to modify the sort order etc... all of the things that are shown in the library settings, but aren't obvious when you go to the knowledge base. Can you guide me in the right direction?
I’m not sure that SharePoint TOC web part is what you are looking for. It displays navigation of current site, not of the wiki document library.
The Knowledge base in Plumsail HelpDesk is just regular pages library. If you want to create table of contents on a page, you can edit this page and add links to appropriate pages in the text editor.
As an alternative, we suggest you to use OneNote as an internal knowledge base of your help desk.You can update right navigation and set link to the OneNote notebook instead of pages library.
If you need more functionality we also offer an ability to order improved knowledge base in our customization store.