Application navigator links missing in Bamboo 5

I just upgraded Bamboo from 4.4.6 to 5.0 and was trying to get Application Navigation setup to work with JIRA and Confluence (each has an application link to each other).

First issue I noticed was that there's no link to configure it in the 'Bamboo administration'. I finally found a link by clicking on a Manage link in JIRA's Application Navigation setup. Once I was able to view the page, I noticed a JavaScript error trying to view it (both in Chrome and Firefox). When I worked around the issue by using the browser's debugger, I was able to view a list of all application links, but there are still no navigation links throughout the Bamboo application in the top nav.

As you can see from the screenshots, I've already had oddities between the app nav configuration with Confluence and JIRA (Confluence wants to have Bamboo twice for some reason), but they still work fine for the normal user. So there seems to be 2 issues that may or may not be related: First: "TypeError: Cannot read property 'type' of undefined" when trying to view http://bamboo/plugins/servlet/customize-application-navigator; second: application navigation links do not show up in the Bamboo top nav.