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Assuming brakes are properly bled, have you considered swapping to a more aggressive pad? OEM pads do NOT prioritize stopping (sounds bizarre, doesn't it?) OEM pads are quieter and make less dust but initial pad bite and friction is usually dismal at best.
Even a car with 14" Stoptechs with an OEM style pad will be outbraked in a single stop by a stock sized setup with a proper Raybestos/Porterfield/Hawk race pad (assuming tires are not a limitation). Pads have a greater effect on brake feel than any size BBK or rotor material.
Start from square one and rebleed all 4 corners + master/ABS. As mentioned before, the general thought process revolves around bleeding the LONGEST lines first and going proximal from there. I personally wouldn't do this without a power bleeder or reverse bleeder but it can be done if you have someone around to help. It CAN'T be done properly solo. Some will claim it can be done but you will end up getting air into the caliper and it can be very difficult to get it out after.
Toyota and Lexus Join Mille Miglia For The First Time
Slideshow: A five-car lineup spanning more than five decades of Toyota performance and engineering will tackle one of Italy's most celebrated automotive routes.