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I have a '06 civic and the front end wobbles when. It really applying the brakes shudders. I have put on new rotors and pads on the front and it cured it for about 5000 miles but it is back worse than ever. Now, I am wondering if I need to change the brake fluid. I also have new tires on with about 5000 miles.
Anyone else had this problem?

 
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You may have warped rotors. I had that happen to my car. I'd brake and the front end would shake like mad. I changed the front rotors and changed my pads even though they weren't too worn. No problems since. You're gonna need to bleed the system anyways, so you'll need a container of fresh brake fluid.
I just realized that after re-reading it you actually did have new pads and rotors. Im at a loss then. I was just speaking from personal experience. You should've bled your brakes after the job. I'd go back and recheck your work.

 
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OK, now I have changed the brake fluid and flushed the system and bled it. The shudder is better but not totally gone. So I have to date done:
1. New rotors and pads in front
2. New tires and balanced
3. New allignment.
4. Changed brake fluid and bled brakes front and rear.

I don't know what else to do.

 
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Just answered the same question on a different thread. Had the same thing happen to me. It turned out to be the front suspension bushings.