If you rotate the display on the TFT, you will also need to rotate the touchscreen.
If you haven't already done so, install xinput.
Open up the X init script
And add these lines;
DISPLAY=:0 xinput --set-prop 'ADS7846 Touchscreen' 'Evdev Axes Swap' 1 DISPLAY=:0 xinput --set-prop 'ADS7846 Touchscreen' 'Evdev Axis Inversion' 1 1
You may need to change the values at the end of the each line;
Evdev Axes Swap
Swap X & Y
1 for yes and 0 for no
Evdev Axis Inversion
Swap the direction on the X or Y plane.
1 for yes and 0 for no. A number is needed for each plane
You may also need to re-calibrate the touch screen for X windows. This can be done by deleting the file below and then rebooting;