It is finally time to upgrade from 2.8.6MU to 3.0MS. I have performed the upgrade on a test instance that was cloned from the live 2.8.6MU installation and identified all the plugins and themes that need to be removed due to incompatibilities. What I noticed is that after going from 2.8.6MU to 2.9.2MU I needed to run the Update to update all the blogs. The installation has about 200 blogs and this step took somewhere between one or two hours, and had to be repeated after going from 2.9.2MU to 3.0MS. Is there a way to speed this up? What do installs with thousands of blogs do?
Also, on the test server I did not have to worry about any users trying to access the system while I was upgrading but I cannot guarantee that no one will try to access live while I am upgrading. Is the best solution to configure Apache to not treat index.php as a default index file and put an index.html in the root folder indicating that an upgrade is in progress? Will I just need to add index.php to the end of any URL for accessing the wp-admin tools needed to conduct the upgrade?
Thanks for any advice and if this information is listed in a FAQ that I was unable to locate, I apologize.