I used American Transmission Exchange in Fontana a few years back and they did a great job. They rebuilt the old T5 that was in the Cobra. After they rebuilt the trans it shifted so smooth. I even had Steve at Powertrain Dynamics ask who built the trans because he said it was the smoothest shifting T5 he'd ever felt. They're a little pricey but well worth it.
http://www.usatransdoctor.com/xfonta...rred_shop_.htm