I was running running JMS 1.2.0 RC 2. I was prompted to upgrade to install patches. Following the instructions in the FAQs, I uninstalled the patches (through the joomla backend, Multisites menu) in preparation to upgrade and my site crashed. The problem is that the site thinks all my database tables begin with jos_ but they don't. I changed the configuration file of my joomla install to reflect the correct prefix (uninstalling the patches must have changed the prefix to the default) but to no avail. Do I need to change a file in multisites with the correct prefix?

the site home page is ourrealvillage.com if you want to check it out.

NO.

When you un-install the JMS patches, JMS restore the files that it had backup in /administrator/components/com_multisites/backupxxxxxxx.
Normally all the files present there are the one that you had in your system before to install the JMS patches.

So when it restores, it also restore the configuration.php file that is present in this backup directory.

JMS does not touch to the DB content.
If you have changed the table prefix in your master configuration.php file after the JMS patches installation, you may probably to edit again your configuratoin.php file located in the master root directory.