How long and how many miles did you have the car before the transmission problem?... A few months ago the gearshift from 2nd to 3rd became very abrupt and rough, and the car would remain in 2nd for longer than normal, often not shifting until I let off the throttle... I had the transmission flushed before Christmas, and a new filter and fluid put in. After I got it back it has become even worse than before...
Because the problem continued after changing the fluid and the filter, and because the TCU is telling the ECU to display a code about incorrect gear ratio, the transmission probably needs an internal adjustment or repair.
I would get an opinion from a dealer or transmission specialist.