What RSE said is basically the way I added a few of the books I posted here and also for parts of the Harvard Classics series. I have four scanners her -- film (slide), flat bed, page, and auto feeder -- that are used depending upon the original source material. OCR programs are by Abbyy, Xerox, and Omnipage. For text editing I use UltraEdit. (As an ex-mainframmer it is the best text editing program I have ever used.)
The conversion from single lines to full paragraphs is often by Stingo's Word macro (available through the MR Wiki.) This also avoids a lot of the broken paragraphs.
Once loaded into BookDesigner, hyperlinks are added for the footnotes (although many are in-line right after the reference), graphics added, and titles (chapter and subtitles) are identified. One sticking point in BD is the need for another size font for captions. Currently any centered text picks up the subtitle attributes. I am studying calibre but I am not yet happy with the results (my html is also poor.) Covers are created in Corel Draw, Adobe Photoshop, or Adobe Illustrator.
Some books are quick, others take forever.
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