What transmission in 1989 4x4 5-speed

the 5-speed is the W56 transmission. if you need to get it replaced you might want to look into the transmissions at Marlin Crawler
if it does need to be replaced, this heavy duty trans is the only one i would recommend

Cam

What exactly is "wrong" with the transmission?

You should have a W56-C, or if the truck has the ADD system it would be a G58.
And yes, knowing what's wrong could help.

His mom was driving it and said that third gear went out, but that was a few years back and no-one can remember what the problem really was. Since it is out I am going to take a little look at it, I'm crossing my fingers on shifter bushings and it was just popping out, or hard to get into gear.

if the transmission does actually have problems just overhaul it these things are very easy to rebuild. get the heavy duty bearing kit.