1. use Sony Content Browser to manually import the files to a new archive. this will regenerate all the metadata as well as the correct directory structure and make the files easier to import. select a location in Browser's Explorer window, go to the file menu, select IMPORT, browse to the .mp4s and import them.
2. Log and Transfer doesn't work on EX files unless you have our L+T extension installed. You can find this under Applications--> 'Legacy Applications' at http://www.sony.com/xdcam-downloads . Note that you can also use Content Browser as your import plugin. When installed you'll see an "import-->Sony Content Browser" option in FCP's File menu.
The import rewraps to .mov whether you use Browser or one of the older plugins such as XDCAM Transfer or the Log and Transfer plugin. The files are not transcoded and remain in the original EX codec.