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I have an 06 Elantra that shift great, except between 2-3. If shifts very laggy/hard. It jerks the car.

Now, I own a 2001 Elantra and had this same problem. I know from experience that it is cause by the speed sensors. So I replaced the Input and Output speed sensors and the problem seemed to go away. It shifts very smoothly between all gears when the problem is not there.

The problem also never occurs when the engine is cold. It only starts after the engine gets up to operating temperature.

I'm not sure what is going on. When I replaced them, I had the battery disconnected and it has been some time since I replaced them that it should be working fine.

No CEL, it is also not throwing any codes. The connections are not loose. So I'm at a loss.
 

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I also have a 2006 Hyundai Elantra with the same problem, almost same conditions in the cold. I went to AAMCO today, and the guy said Hyundai recommends resetting the computer as a first step, for this particular 2nd to 3rd gear issue. He charged me $150 for this. It worked.
Now, the transmission is fine.
He said if the problem reoccurs, he would rebuild my transmission, but not replace it. He will take off the $150, if I come back with the receipt.
I thought he was honest.
My car has 159,000 miles.
He could have just told me I need a new transmission.
 
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