First of all: BACKUP YOUR CONTACTS!!!
Then go on... ;-)
You can get the source code here:
SourceForge.net: Funambol Zimbra Connector: Downloading ...
and the instructions for building here:
SourceForge.net: zimbrafunambol » build_from_source
Then replace the original ZimbraConnector.s4j with your custom one and run install-modules as documented in the installation guide. Do not recreate the databases or you will need to reconfigure the data sources in the Funambol administration tool.
For debugging purposes you can raise the logging level of Funambol to DEBUG (in the admin tool) and issue a "tail -f ds-server.log" to see what is going on during a sync.
Good luck!
Daniel