<blockquote> I've trimmed down the default to "Assignments" but whenever
I create a new class and try to customize the layout, I can always
add "Lecture Notes" as well as "Handouts" eventhough it's broken.
</blockquote>
Are you editing the dotlrn-fs.info file or setting the dotLRN File Storage Applet's param through /admin/site-map? Editing the .info file will not work except at installation time. Using the site-map
works ok for me.
<blockquote> user_portal_pages_csv seems to be ignored also as the user
portal pages are always named "MySpace-Calendar..."
</blockquote>
This parameter sets up the pages and layouts for the _user portal template_ at dotlrn installation time. Each time a (full) user is
added to dotlrn, a one-time copy from the user template to the user's template takes place. If you edit the user portal template at /dotlrn/admin/portal-templates, then create users they will get the new values.
default_class_instance_applets may be buggy. I'm looking into it. As a workaround, you can hide the FAQ portlet from the class portal template (/dotlrn/admin/portal-templates) or the specific class's portal ("Customize layout").