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1) Do you think it would make a difference if I had a list of bookmarked links I made up myself vs. the standard Word table of contents? I did a draft where I used my own (manually-created) links on my own.
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I think so. I have long, single-page documents that I cleaned up and formatted first in Word and then saved to html. I just inserted my own bookmarks in the places I needed them (using MS Word), and then clicked the box for generating bookmarks based on "Named anchors" (which can also be the usual bookmarks found in an html document).
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2) Do you think anything on the iSiloX tabs would help? I nosed around in the 'Bookmark' tab and found 2 options: one called 'HTML file' which looks like it would resolve all your bookmarks to one file (is that true?) and another called 'Named Anchors' which looks much more promising, but I cna't seem to get it to do anything for me. Do you know how 'Named Anchors' works?
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No, it doesn't resolve all your bookmarks to one file. What I do is create a TOC page, where the hyperlinks to the other pages are. Then I use that page as a source, and click on the "HTML file" box and point to that same file to tell iSiloX to generate my bookmarks based on the links in that page. Then I convert that page with link depth set to "1" and I get all the linked pages as well, with a list of bookmarks generated from that same page.
Hope this helps.