Have you looked at the Vehicle Speed Sensor? Sometimes, especially if it has some mileage on it, the sensor will pick up fine metal shavings on it. This condition disrupts the signal to the PCM.
Agree,The first thing I would do is put a scanner on its and see when the actual comment for the shift is being given. Any real scanner or tuner should be able to see this informaton live while doing it. Shift timing issue are far more likely to be a car control issue than an actual trans issue,
Frank at PerformaBuilt