Thanks both for the insight, and Tex for the very comprehensive post
I started with the PDF version as I noticed the other formats were really dreadful and I had confidence in my ability to master ABBYY quickly.
Now that I have a better vision of the whole project I think I'll head the Word route with Toxaris' tools and see how it works out, preserving the original layout with the side columns.
I do like the idea of inline sidebars too, although at that point you would also have to trim them to avoid fragmenting the main text too much. Or maybe a more elegant and modern solution would be to simply italic or bold the keywords within the body text , since their main purpose seems to aid finding a particular paragraph while skimming through rather than adding information.
I won't follow your advice on the project though
Now that I'm involved my curiosity and willingness have gone up and, since I don't have any deadline or standards to meet, I can take it easily and have a relaxed pace.