Your setup looks OK. Let's first confirm that the device is still functioning properly. Go back to the 'blank' sketch and wiring configuration you had before and make sure you can still talk to it with the SFG tool.
This is very strange. The device works and the pins work for serial communication. We also know that the library and examples on Github work (it hasn't changed in 6 months).
So, either you have a corrupted copy of the library (Try re-downloading it), or something on the device has changed. Check with the SFG tool that none of the default setting on the device have changed (e.g baud-rate).