I will check my Mazda manual so will tell you exactly what you have to do, if I remember it's very easy, just it takes time (like 1h).
For the window:
1. Ignition ON
2. Select all windows and open all windows with the switch
3. Select each seat/window separately
4. Close the window and KEEP holding the close button for another 2 seconds after the window was closed
5. Repeat from step 3 until all windows/seats are configured
For the ECU:
I can't find it in the manual, but in essence it is that you have to let the car re-learn the conditions/degradation of its components. Maybe before you did the disconnect it was for shorter period of the time and it didn't wiped, or the car was in better condition so the difference was not that big.
1. Turn all electrical things off, no blower, no A/C, no radio, no lights.
2. Find safe and level place, hand brake on
3. Turn the car on, let it run for 20min - 30mins at idle, do NOT touch anything.
4. Then turn high beams, A/C, full cooling, max speed of cooling, radio and all electrical appliances (fog lights, everything you have which could increase the load on alternator and the engine)
5. Let it idle for another 20- 30mins, do NOT touch anything
6. Go for a drive, the problems should be gone or be better.
I know it sounds stupid, but id does work, if you do not want to do it I think the car will learn it anyway eventually as you are using it.