Here is another guide from @brotherchris:
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"...and their rotation script doesn't work..." 
Okay, the screen is now rotated but he didn't mention the TFT orientation part. Alright, he finally got to that.
I don't love re-orienting the TFT in x11 but leaving it wrong at the console level.
Thanks for posting this!
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Hello Chris and welcome to the show 
@brotherchris Read through this issue on the Adafruit repository for their script. It's a conversation with Lady Ada herself regarding the duality of controlling display+touch in both console and x11.
My complaint with her and other resellers/providers then is that they almost always skip over the console-based drivers and orientation (for both display and input device) of the TFT displays and then just handle this in the x windows system. But for Raspbian Lite installs (especially with Kivy, say), you really need everything setup correctly without all that Desktop stuff.