We have a 2004 PreRunner and have issues also. The front end shudders under heavy braking. I replaced the pads and turned the rotors, felt okay for a few thousand miles, and it came back. I put brand new rotors and new ceramic pads, it felt okay for a few thousand miles and its back again. Behaves like a warped rotor, but I simply cant believe those two new rotors got tweaked just that fast.
Im gonna pull a tire off tonight and put a dial indicator on the rotor, spin it and see if its still in spec. Ive read that if the rear drums/shoes arent working well that can causes issues so I may end up replacing those to rule that out. Thinking about flushing the brake fluid also to take that variable out of the equation also.
