Very sorry for the delay. We'll have the updated release(s) for 2.5.5 and 2.5.6 out within the next week. There were some minor issues with this new release from Joomla. Honestly, the 2.5.4 check should check most of the really important (and commonly hacked) files. I'd start there and see if that doesn't report too many false-positives.
Never fun being hacked, we understand, and again, sorry for the delay.
I just posted a new version for Joomla 2.5 which checks for 2.5.5 and 2.5.6. You should be able to download it from our extensions page: http://www.sourcecoast.com/free/free-product-overview
No, Version Verification Tool will not detect extra files on your site. It will only detect if original Joomla files have been changed or are missing altogether.
If you're looking for more of a 'hacker' scan, you may want to look into Admin Tools Pro from Akeebabackup.com. That has a malicious file scanner which will check *all* of your files for changes (vs the last time you ran the scanner) and also has a check for 'malicious looking' files. There's still some manual intervention necessary to check the files it thinks may be bad and for you to investigate further.
We use Admin Tools Pro for various reasons and think it's great, and would highly recommend it!
Best of luck getting your site back on track,