I did try it after adding the index and it was better, but not by a huge amount. The rewrite really helped.
The missing index.... I'm not sure what to do about this. I was thinking of filing a bug report. The problem is that acs-content-repository/sql/oracle/upgrade-4.6.1-4.6.2.sql doesn't work; it has comments at the ends of the lines, after the semi-colons, and Oracle can't handle that. So our sites here at Sloan didn't have any of those indexes.
I can fix and submit the file easily enough, but that isn't going to help anyone who has already done the upgrade. So what's the right thing to do here - write a new upgrade script?