Hmm, did all of the directories get uploaded? If you'd like, go ahead and open up a support ticket with your site URL and the FTP info and we can take a look at what's going on.

One thing I did notice is your PHP include path:

(include_path='/usr/local/php/includes:/usr/local/lib/php:/usr/share/pear')

It's not including the current directory. Normally that would look like this:

(include_path='.:/usr/local/php/includes:/usr/local/lib/php:/usr/share/pear')

Basically now you need to do the import. You'll download the threads_import.zip file from the members area. Unzip and place that inside your importers directory. Bring up the importers/threads_import.php script in your browser, fill in the info and it should import all of your data.