Hi cptnemo,
the previous observations are correct: besides technical things, like internal links and the like (have you tried validating your EPUB, after creating it?), the file/TOC/OPF-content size might be a problem for most readers. I second the previous suggestion of trying splitting the files in smaller EPUBs, e.g., by starting letter.
I did a similar, but smaller in size, project by fetching the Divina Commedia with several commentaries from the Dartmouth Dante Project (you can get a proof-of-concept here:
here), and packing it into a single EPUB (the resulting EPUB is roughly 3 MB, with 100 XHTML pages, and 10,000 notes/comments).
I am quite busy these days, but mid next-week I could give a look at it, if you like to work on this 'project'.