I got an 87 runner 22re with LC's cam, crank (stroked) and Headers. I get troubles idleing sometimes and I've narrowed it down to having the brake applied while stopped or decelleration like coming up on a red light.

I know there is a connection that tells the motor to mellow out when the brake light comes on so I was thinking a new connection needed to be made oe something.

 

Check the booster vacuum line. Sounds like a vacuum leak there or in the booster itself.

 

You're right on. The ECU cuts fuel when the brakes are applied AND the idle speed is at 1400(?) rpm. If your idle speed is high (even a couple hundred rpm) this feature on the ECU will cause the engine to surge. Check your idle speed and set to the appropriate speed of 750rpm.