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Try cleaning out the throttle body too.
A dirty throttle body can make your whole car vibrate when you brake at random times.
Use a throttle body cleaning spray, pick it up at car parts store. Wipe it out after spraying and make sure to clean around the flap as well. Keep doing it until it is clean.
If you need further instructions about it, ill post them.
If this does not help, check all your brake pads and shims again. See if the rotors are worn as well.
I've had experience with this problem so this may help.
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