The ECU doesn't change the open loop maps. Thats why they are open loop, it doesn't adjust these mapping values.
Yes i think your better off to make your changes in the open loop areas like on boost. This is where you will see the most gains in terms of power. Closed loop areas you arn't making any real power and they are closed loop for fuel economy and emissions and are best left to what toyota has already setup.
Generally leaning off the af ratios at full sing is required. Giving some aditional advance provided no detonation will occur will give you fists full of power
Re-booting wont damage the ECU at all. Do it a million times, it wont affect it.
Reset the ecu after changes like exhaust, pod filter etc. After you have had a problem, the engine light has come on and you have definitly rectified the problem. You dont want it storing faults that you know are already fixed.
To reset just remove the negative or positive battery terminal for 30 secs then put it back on.