I'm using 3.3.0. I'm able to get book stats if I click on Extras>Reading stats but that only shows statistics for the book I'm currently reading. Is this the feature that is broken for you?
I don't know that it matters, but I'm using the default drivers that came with Calibre 1.44. I found that the extended Kobo drivers and the Kobo utilities plugin were corrupting my SQLITE database. Not sure why, but the behavior of the driver and utilities were consistently bad.
I have both default drivers (Kobo Reader Device Interface & Kobo Touch 2.1.7) set to only accept KEPUB rather than EPUB, so that Calibre automatically converts all of my EPUB files to KEPUB when sending it to my ereader.
As far as synchronizing only the books you wish, try logging onto your web account, go to the "I'm Reading" part of your library, select the books you don't wish to synchronize, and click on the fuchsia "DELETE" button. I know that sounds scary, but your books will be stored in the trash until you permanently delete them. Then, only the books remaining in the "I'm Reading" part of you library should synchronize.
One
VERY important disclaimer: I'm not sure if there is a time or space limit on the books Kobo allows you to store in the trash. I tried this for a week or two, and all of my books remained there, safe and sound. You might only want to try this with a few books you don't care about to see how long they stick around (keep backup copies, of course).
Maybe a chat with their staff would clarify this?
I now use a dummy user profile and I sideload all of my firmware updates and dictionaries. So, I can now rely solely upon Calibre without using Kobo's servers. Consequently, I've moved all of my books back into the main part of their web library. I like not having to depend on Kobo's servers to sync my books, dictionaries, and firmware updates. As you know, it takes forever.
But, that involves doing a bunch of technical acrobatics. Some folks enjoy that sort of thing and some don't.
Hope that helps?