New Post Editor format messed up after 3.9.1 upgrade

The new post page (and new page page) editor is formatted oddly. Buttons appear in the sidebar, and the edit field is oddly sized.

I’ve tried:
1. Deactivating plugins
2. Changing to 2014 theme
3. Clearing browser caches for all browsers on machine
4. Re-uploading wp-includes from a fresh 3.9.1 download
5. Ticking disable visual editor on and off for my profile

None of these resolve the issue. I’ve also tried various orders of doing the above.

When I look in the browser console, these are the errors:

GET https://tsukata.org/wordpress/wp-includes/js/mediaelement/wp-mediaelement.css?ver=3.9.1 404 (Not Found) post-new.php:31
GET https://tsukata.org/wordpress/wp-includes/js/thickbox/thickbox.css?ver=3.9.1 404 (Not Found) post-new.php:29
GET https://tsukata.org/wordpress/wp-includes/js/mediaelement/mediaelementplayer.min.css?ver=2.13.0 404 (Not Found) post-new.php:30
GET https://tsukata.org/wordpress/wp-includes/js/imgareaselect/imgareaselect.css?ver=0.9.8 404 (Not Found) post-new.php:32
GET https://tsukata.org/wordpress/wp-includes/css/editor.min.css?ver=3.9.1 404 (Not Found) post-new.php:298
GET https://tsukata.org/wordpress/wp-includes/js/thickbox/loadingAnimation.gif 404 (Not Found) load-scripts.php?c=1&load%5B%5D=hoverIntent,common,admin-bar,schedule,wp-ajax-response,autosave,sug…:71

Note that I’ve temporarily set the theme back and re-enabled key plug-ins, so if you visit the site, you’ll see that it’s not in barebones state right now. If I get another troubleshooting idea, I’m happy to disable again to test.

Ideas welcome!