SharePoint Site Design & Implementation: "Online Manual"

I am looking to create an "Online Manual" site template in MOSS 2007, in order to create a number of sites that will hold static information on an array of topics.

What site template should I use, I am currently thinking Publishing Site, but a Wiki might work?
How should I show the navigation for the different "Chapters" (in the left side panel)? I could use the "Table of Contents" webpart, a custom view on a list, or something else.
How should I store the created "Pages", 1 large Page Library, or separate Lists for each "Chapter"
Lastly, Should I just hard-code the navigation webpart to the master page so it appears on every page?

EDIT:

My real issue is "How I am going to create the left side navigation, to be shown on every page?"

It should be a Table of Contents type of view that has all of the pages grouped by chapters.

Solution

Thank you everyone for your help! I just wanted to let you know what I ended up doing to create the "Online Manual".

I created a custom

1) Master Page to allow for the desired 2-column layout.

2) Page Layout to persist the navigation control on all pages.

3) Document Library with "Chapter" and "Sort Order" custom columns

4) Web Part (in C#) that uses the object model to retrieve all pages from a document library and display them in a list grouped by "Chapter" and sorted by "Sort Order"

I used the Publishing site template to allow the contributors more freedom to create content.

Thanks again!