The IA Upload tool now will work with files over 100 MB.
Example of large file uploaded: https://commons.wikimedia.org/wiki/File:Once_a_Week,_Series_1,_Volume_X.djvu (278.92 MB, 736 pages).
Sorry this took very long. There were a few steps to getting it working.
Let me know if it fails for you!
:)
Thanks, Sam.