96 Ford escort transmission bad?

My dad owns a 96 Escort. He had some electrical problems with the radiator fan. The connector was melted and he finally got the connector removed and tried to troubleshoot it himself. In the course of troubleshooting he managed to short something and it caused a lot of electrical problems, including smoke coming from the steering column. Wound up the motor wouldn't go off, among other things. Well, he took it to a shop and got the electrical straightened out, but now the transmission only works in low gear (automatic). Ford shop told him he needed a new transmission. Is this a certainty or are they just trying to get money out of an old guy? He said they put it on an analyzer when they tested it. Could it be that the computer in the car is bad and not the transmission? Thanks. Brian