Two more little suggestions...
1) Make the title page and TOC optional. Right now, before generating LRF from HTML with the tool, I make a copy of the HTML file and remove the title page and TOC from it if they are already there, then run the tool on it using the edited copy. The output is also inconsistent with purchased books, which have their book cover on the first page, followed by title, TOC, etc. If my HTML file has a jacket cover at the beginning, it's currently displayed after the auto-generated TOC and title pages.
2) Complementing 1)... if the HTML has local links (ie, same or no document name and linked to an anchor using #), make them active. Lots of HTML docs have a TOC and/or index built into them already using exactly that method. Currently, BB builds it's own TOC, which it puts before the one already in the HTML file... from which links have been removed. Looks odd to see two TOC in a row, esp if the pre-existing TOC was single-spaced and is now all mushed into one paragraph.
Just my thoughts - also willing to lend some coding if you need a hand, though too many cooks could make things a little crazy as well. (also, I already tried loading your project... I'm a version of VS behind you and it won't let me load your new-and-I'm-sure-improved solution file)