Thanks for buying my book!
Check the TVs to make sure they are connected to the appropriate templates. If there are no TVs connected to the template a page uses, the Template Variable tab won't be displayed when editing that page. While you're checking, check the category of the TV to make sure there's a category with that name or ID. If it's invalid, that might also hide the TV.
If that's not it, before starting over, I could try re-uploading the files as described here:
http://bobsguides.com/modx-upgrade-faq.html. Then run Setup again.
Another approach, rather than starting over, would be to revert to the previous version (you did back it up, right?), and upgrading to the intermediate versions one by one, running Setup each time, again using the technique above to upload the files.