1989 Trooper Transmission

My son lost hydraulics to his clutch slave cylinder in his 1989 Trooper 4X4 and he pulled the shifter very hard into second gear so he could make it home. I then replaced the clutch slave cylinder for him so now he has a clutch pedal again, but he only has second gear and reverse now. The shifter is about 3 inches lower than it was originally in second gear and the shifter is almost hitting the seat. Does anyone know what the problem is?