Is there any shudder at higher speeds when brakin? Shudder like that when braking is more likely to be warped brake rotors, the D40 rotors are known to be soft and therefore prone to warp. Be the easiest and cheapest solution, just get the rotors machined(if still within spec) and some new pads.
I have 2x autos and they both seem to pulse(surge slightly) during the last few metres before the car comes to a complete stop, there doesn't seem to be any issues with either.