Same exact problem here. I had so many problems trying to get AD working with 4.9 I decided to give 5.0 a shot...but can't even get it to install by default. I tried this a few days ago by installing the AD provider AFTER RC2 was already installed, but there was no Authentication menu item under the Admin menu. :(

I realize this is an old post, but I ran into the same error message ("FCKeditorAPI is undefined") while trying to install the Active Directory Authentication package, and found a workaround.  Forgive me if it's not ideal, but my experience with DNN is all of three days now.  Incidentally, I'm using DNN 4.9 and FCKeditor 2.6.3.

I temporarily edited one of my skin ascx files to include this line near the top (right under the "<%@Control ..." tag)...

<%@ Register TagPrefix="dnn" TagName="HOSTSETTINGS" Src="~/Admin/Host/hostsettings.ascx" %>

...this line in the body...

<dnn:HOSTSETTINGS ID="HostSettingsControl" runat="server"  />   

...and these lines at the very bottom:

<script type="text/javascript">
    //<![CDATA[
    function Webform_OnSubmit() {
        return true;
    }
    //]]>
</script>

Then I logged in as host, accessed a page that used that skin, and successfully installed the AD package.  Including that HostSettings.ascx control gives you the tools to install that authentication provider, and the dummy JavaScript function at the bottom serves to "override" the built-in JavaScript function that erroneously references FCDeditorAPI.  Maybe not an ideal solution, but it worked for me!