We check this website, now kyoto-u.ac.jp is up and dont blocked for our system and other users of the Internet.
So, answer to question: Is kyoto-u Down Right Now? - NO! kyoto-u is up!
If you have problem with access to site kyoto-u, and domain kyoto-u.ac.jp is not avalible.
Clear browser cache and/or try other web browser
(Chrome, Firefox or Safari).