Hi danscott,
1: This appears to be a bug, and I've submitted a bug report (
http://pkp.sfu.ca/bugzilla/show_bug.cgi?id=7232) to ask that the url in the prepared email directs the author to the Editing page rather than the Summary page. You can add yourself to the cc list to get updates on this bug.
2&3: Make sure that you have the prepared email enabled for COPYEDIT_AUTHOR_COMPLETE. When the author finishes her/his copyedit, s/he has to indicate it’s completed by clicking on the envelope icon under Complete, which generates an email to the editor. Once the author has done that, Step 3: Final Copyedit step will be highlighted.
Hope this helps.
Lisa