You're being very complicated! OCR the text, check it, strip it down to the most basic un-formatted style (dropping it into Notepad is an easy way).
Paste the text into Sigil. Split into chapters. Add the minimum necessary formatting - a header style for titles that should be in the Table of Contents for instance.
If there are further hyperlinks required, edit them in.
Forget about a linked index - just use a word list. Every reader device or program has a Search function.
Footnotes are a problem, as you don't have control over pagination in an eBook. Decide whether they would be best inline, in a block at the end of each chapter, or in a chapter of their own.
Don't try to be clever. Don't try to produce a fascimile of the printed edition. You're not laying out pages, you're pouring text into a container.
Don't give the job to someone who can't cope with basic HTML editing.
This is a BIG job :-)
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