Need Help Tranny Swap Check Engine Light..

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Check stored fault codes first.


Also, if it was a proper swap, the ecm should have been swapped with a manual ecm.
pull the passenger side kick panel and ecm code.
it is printed on a sticker on the side of the ecm.
 
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Check stored fault codes first.


Also, if it was a proper swap, the ecm should have been swapped with a manual ecm.
pull the passenger side kick panel and ecm code.
it is printed on a sticker on the side of the ecm.

Exactly what davis3 said. Pull the codes! Then you will know what is up! Could just be an unplugged O2 sensor or something. Worse comes to worse, pull the CEL bulb. I had to do this with my engine swap due to and IAC out of range and a TPS voltage code. Passed inspection just fine.
 
I suspect this a non compatible transmission speed sensor issue (OSS vs VSS). The 98 and older Mustangs use a VSS sensor. The 99+ uses an OSS sensor. The two sensors are not interchangeable (totally different signals) and need to match the PCM and wiring harness.

Research a tail shaft swap or an "extended range" SpeedCal.