some of the vibration will stay, first check the mounts, second thing would be to scan the ecu and find out whether everything is perfect, i have a feeling that something is wrong with most 1krfe vitz, they don't give good enough fuel average and they vibrate, i feel it is something related to valve clearance, vvti or sensors
the vitz service manual shows a detailed troubleshooting flow chart. that should be implemented.
i feel that the vibration might be a slight misfire