Typically the only issue from switching from 32 to 64 is with the reporting graphs (search the forums for graphs). I'd suggest backing up your config as well as the contents of your jail and doing a fresh install. After installation, you can restore your config. Since 8.x apps are incompatible with 9.x apps, you will need to reinstall them anyways, so you may be better off creating a fresh jail, installing your apps, and restoring your app configs from your jail backup file.
Note that jails changed significantly from 8.x to 9.x so it is well worth while skimming through both the Plugins and the Jails chapters of the 9.x PDF on the FreeNAS download page. That way you can determine which install method best meets your needs regarding the software you plan to install.