The custom permission deletion has been added recently to acs_object.delete in the oacs-4-6 branch. There is no upgrade script for that, but dropping and recreating the pl/sql package should do it - I guess with Don's new permission stuff there will be an upgrade script that drops and recreates the package anyway.
And I don't see the difference between these two:
delete from acs_permissions
delete custom permissions
Did you mean: delete from acs_privileges for the first one?
