From what I'm reading above, it sounds like an uninstall and then re-install worked for you and you're good to go on the site with the fatal error, correct? If not, let me know so we can knock that issue out.
In general, when moving from Joomla 2.5 to 3.x, I'd recommend:
* Uninstalling JFBConnect (your settings will still be intact)
* Performing the Joomla 3.x update
* Re-installing JFBConnect
A direct upgrade to Joomla 3.x *should* work though, and I'm not sure why you ran into issues. Re-installing JFBConnect (even without uninstalling first) should also be a viable option as that will re-install all our files and run through our installer routine, which will check for any inconsistencies. That process can never be 100% fool-proof with the number of server and Joomla configurations, but it works very, very well.
My only guess is that there were some file/directory permission errors on your system that weren't letting our files be read. By uninstalling, all our files would have been deleted... then re-installing would have replaced them with the correct Joomla permissions.
I hope that helps explain and get you going. If you have any other questions or run into any issues, just let me know.
Thanks,
Alex