I'd say keep it very simple.
I find there's nothing worse than a text-packed site based in a busy template. Make it simple, clean and easy to read.
Use good spacing, keep away from long paragraphs and try as much as possible to break the content into managable chunks.
As for navigation I personally would go with 1 simple menu, listing main sections, a more indepth expandable menu (js, dhtml) and a site map link on every page.
Make sure to have a site search facility also.
"I tried the black/dark gray text on white/tan backgrounds, but found it to be very harsh after an hour or so of reading."
I doubt many readers will stay online reading for an hour, more than likely they'll download the page, print it or copy/paste. either way keep it simple, clean, well spaced out with good clear fonts.
And don't make the text too small!!
If your content requires a lot of images then make sure your template has minimal images. Set yourself a maximum size of page and try to stick to it. Loading time is very important as we all know.
That's all I can think of for now.
SSI is a good way to go but can be heavy on the server, depending on how many pages will be parsed. 60mb of text, number of pages?
An alternative to SSI would be PHP but you definitly need to use some sort of template system for such a large site, ssi is the easiest.
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