I've already uploaded my collection. Unfortunately they also have a 50MB limit which excludes several of the books from the Humble Bundle eBook collection.
Not sure if this would work, but it offers to let you "upload" from an existing Google Drive folder. I wonder what would happen if you added the >50MB file to google drive, and then selected it from its Drive location in the books uploader UI.
The largest files I have to test area 40MB PDF and 35MB Epub, which worked. I tried a 100MB iso renamed to pdf, but it seemed to detect the right mime type and excluded it
