We have FTS3 working very nicely on 150,000+ records. We are getting subsecond query times returning over 200 results on a single keyword query.
Presently the only way to get Sqlite FTS3 working on the iPhone is to compile your own binary and link it to your project. To my knowledge, the binary included in your own project will not work with Core Data. Perhaps Apple will turn on the FTS3 compiler option in a future release?
You can still link in your own Sqlite FTS3 binary and use it just for full text searches. This would be very similar to the way Sphinx or Lucene are used in Web App environments. Note you will still have to update the search index at some point to keep synchronicity with the Core Data stores.
Good luck !!