@Tex2002ans
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Edit: I just thought of this potential solution. Since you already have well marked HTML, but are only missing the auto-generated #s. Would it be possible to have Sigil carry you most of the way? You can have Sigil auto-generate a toc.ncx, you can then come up with some sort of script to manually add in numbers to each navpoint. Code samples of everything could potentially help us iron out problems (a typical chapter, your HTML TOC, your CSS, the toc.ncx, ...)!
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File under 'Blue Skys' -- I often thought that a 'post processor' plug in or standalone program would / could / should be able to handle a lot of the 'not in epub2' questions.
Kind of like MS Word's Bookmarks
For example in the epub you could have what the epub sees as just text
{{SomeVariableName=Cats And Dogs}} to 'store'
and
{{=SomeVariableName}} to have the postprocessor replace it with Cats And Dogs at that point in the epub
CSS counters only work within a html file (I learned that here)
You could do simple epub level math
{{ChapterNum=1}} to 'store' a starting value
and
{{ChapterNum+1}} to increment and update to call accross multiple html files
Generating a SIgil TOC after running the PP would now pick up the replaced text
Oh, well
Paul