I have the exact same problem that you do: violent shuddering while applying the front brake. I changed my brakes from Avid Shorty 4s to the new Shimanos, in attempt to solve it (and, yes, I have toed my pads in, out, cleaned my rims, tried different pads (kool stops included)). Less squeal but shudder remained
I believe that the fork is flexing back and forth, struggling to remain straight from the power of the brakes, and THAT is the shudder. Does anyone agree with this diagnosis? Would a stiffer, or different, fork solve the shuddering?