Finally, I got it sorted today and thanks everyone for the help. So, it is just air in the system after all, and the mechanics I went to have an ATE pressure bleeder and got all the air out in the first go. However, they were just checking the work done and also found that the pins and spring on the rear brakes wasn't inserted properly, and they have fixed the loud click that I have.
So, that confirmed Brembo did a fantastic job in engineering the part to suit stock MC and a larger one is not needed for a brake upgrade if the kit doesn't come with it.
So hopefully this will help someone to diagnose the problem if they have similar issue.