Hello. Been having some issues with my Lexus idling at red lights. It will jerk back and forth until I turn the AC off completely then it stops and idles normally. Its been doing this for a week or so now I had been having alternator issues but replaced the alternator last night and it's cranking strong and driving good. What could be causing this jerking motion with the AC on? It sounds like something clicking on and off when listening from the outside.

 

The clicking is probably the compressor turning on and off, which is normal, as long as it's not doing it at a fast rate. I would first check your voltage, with the car running and the ac on to see how your voltage is.
Does your car jerk when in park or only in drive, with your foot on the brakes, idling?

 

Most likely caused by disconnecting the battery when you replaced the alternator. When the battery is changed or disconnected, the ECU loses it’s memory, and the electronic throttle (drive by wire) system resets to the original new vehicle stored values. Most times the relearn process is completed in 50 miles. If it does not, it may also require a throttle body cleaning to return to normal idle.