I wonder why that Vitz vibration topic is locked.
but as the OP said faced loss of charging voltage causing the ECU to go haywire and installed something additional. Along with change of alternator.
If the alternator was failing to charge at 14V and the voltage regulator was good inside it then the only cause of lack of charging is
1 - flaky reference voltage to the alternator
2 - bad ground to engine.
3 - bad battery main fuse.
Very usual cause in these accountant engineered cars (vitz/passo/boon etc etc etc) - they use the smallest gauge wire in the least possible length to save money.