Same Problem
Steve,
I installed a new T56 Magnum in a 2003 Mustang Cobra this spring and am experiencing the same issues you described in this thread. Were you able to resolve the issue and if so what did you do? The shift from 2nd to 3rd will catch when cold and becomes nearly non existent when the transmission is heat soaked after driving for awhile. The transmission now has about 2000 miles on it.
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