almost right, there can be an issue with 4th gear not engaging due to swarf build up, this affects manual boxes as well.
If they have messed up the ECU they are readily available from a breaker as they rarely go wrong, but it is more likely as Loknar says, there is a damaged sensor of something not connected up correctly, they could also have damaged the multi-pin plug during the dismantling process
Which gears have gone AWOL? and did the new box come with a new actuator, or did they transfer over the existing one?
Is not that seles are more awkward to work on, they just show up the failing of poor mechanics that bit more readily than conventional systems.
How far from WAD in Wolverhampton are you?