Well, I thought I should update everyone as I am at 5700 miles now (1000 miles on the new engine). Sadly to say, the rattling problem is something I will have to live with. I have heard the rattle 3 times on the new motor. Not bad considering I used to hear the noise almost everytime on the old motor.
Since replacing a bad clutch master cylinder, it is not as smooth as it used to be. Nothing was done at the dealer since it was "up to spec". You can't really notice it until you depress and release the clutch slowly.
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