waja stock brake sux big time. i've tried changing to ferodo zero and bendix metal king titanium pad coupled with cross drill / slotted / ventilated disc (front, with stock caliper), pro-rs brake hose and brake fluid bleeding but the performance is still not up to expectation even at optimum operating temperature.
swap with perdana brake system front; still not up to the mark. finally settled for twin pots evo 3 brake system. takes a lot shorter distance to stop, even in high speed 
if the disc surface is uneven, it will caused a loud squeaking sound when we press the brake pedal slowly.
skimming the disc will settled the problem but for safety reason,  it's not advisable to skim the disc more than twice!
if the pedal need to be pump in order for the brake system to works properly, bleeding /changing the brake fluid will help.
it's normal for the ecu to take a couple of days before it adapt to the new changes / lcp.
any big different in acceleration?
how old is your waja campro? my old waja 4g18p's nvh is better than the 1st generation vios when cruising at 160km/h. i am comparing both due to to the car's age
check your engine mounting / bushes and those absorber bushes/ top cover(rubber).  an all round noise insulation job cost under 1k nowadays; and the material is a lot more lighter than it used to be a few years back.
waja 4g18p with airbag was the premium (X) version. beside the airbag, it does come with abs , leather seat and climate control. scroll to page 1 for more.
squeaking metal sound? or rubber sound? 
you should try a reputable brand of adjustable
tein superstreet never fail me after more than a year in use. but the ride is harder compare to the stock
setup 
currently looking for a custom made spring for it.
must be an uncomfortable ride then. consider changing it to metal type