When you swapped the trans did you swap the trans range sensors also?
Some remans come with it others dont. The sensor is located on theh transmission were the shift linkage is and when you change gears the sensor tells the computer what gear you need. If they short out than they can lose gears.
Do you have the sensor from the 94 to try on the 96?
According to the Motorcraft website they are the same transmission so as far as the trans being wrong you are ok. But if the new trans did not come with the sensor i would get a sensor and try that.