why would you want to throw in a transmission thats known for being faulty? Suppose you could use the 94-97 auto, but then you'd need that ecu for the right shift points and a SAFC to get the A/F right..
Anyhow as for ECU, yes you'll need one off of a 98-02 4 cylinder automatic. you'll also need to modify the engine harness to accomodate the auto tranny sensors as well as add new wires to the harness to the ecu. And since the accords have an immobilizer, that means either grab the key, immobilizer ring and ecu off of one car and use that to run the car, or a trip to the stealer to have the key programmed to the ecu..
Grab the instructions on how to swap from auto to manual, and reverse engineer the instructions. you probably could keep the manual pedals though.. just the clutch pedal would be useless.
Would be cheaper and simpler to just buy her her own autotragic accord or teach her to drive stick.