Permissions should be limited to news.ycombinator.com, news.ycombinator.org, and hackerne.ws, each with both http and https.

Change your manifest from:

  "permissions": [ "http://news.ycombinator.com/", "http://news.ycombinator.org/", "https://news.ycombinator.com/", "https://news.ycombinator.org/", "https://*/*", "http://*/*" ],

To:

  "permissions": [ "http://news.ycombinator.com/", "http://news.ycombinator.org/", "https://news.ycombinator.com/", "https://news.ycombinator.org/", "http://hackerne.ws/", "https://hackerne.ws/" ],

        $('tbody:eq(0)').css({"position":"relative"}).prepend(box);

This makes the topbar collapse if you're using userstyles that affect the topbar. I'd suggest using position: fixed instead and not modifying the page CSS.

The script breaks on trying to view my own profile. The error is: "Uncaught TypeError: Cannot call method 'split' of undefined" in chrome-extension://daljejehnbbbhjlecjgafnnfgilbkdhj/script.mini.js:32