Mandatory:
Swap the following electronic components from the '93 transmission to the new one:
MLPS
TCC Solenoid
...and do one of the following:
1. Re-arrange the pins on your bulkhead harness (the main electrical plug for the transmission) so they match the new transmission's PCB.
2. Remove the PCB, and swap the wiring harness from your '93 transmission into the new one.
If you're swapping in a 2000-2002 Mustang transmission, you'll also need to buy either a speedometer gear with 20 teeth, or a SpeedCal.