You are right that the quality of the scans is paramount! Unfortunately I don't have access to the physical books and have to work with the scans as they are (they're not good). But I will look at Scantailor, it looks interesting.

For now I reconstruct paragraphs in html but I could do markdown just as well (where paragraph breaks are marked by double line breaks, and single line breaks don't count).

Collaborative proofreading would be cool but it would require some way of properly tracking who wrote what, and I'm not sure what to use or if I should build a simple system from scratch. Do you have recommendations?