Manual mode shouldn't be affected by any "learning curve" adaptations. Manual mode should allow you to select any gear, however the ECU will over-ride your selection in certain circumstances.
Have you noted that a "panic stop" in manual mode will leave the transmission in 1st gear? This is a safety provision so you can drive out of the way of "the second bus".
For ECU/TCU reset, I've read that you also need to activate the brake light after disconnecting the battery to discharge any capacitative voltage remaining.