The first thing I would do is look at the track the window slides in, there maybe something obstructing the glass or the it might just be dirty. Second, (you'll need to pull the door panel for this one) get a wiring diagram for the window motor, switch and everything involved with the power windows and look for broken wires, tell tale signs of heat, broken connectors and wire damage. With the amount of heat you are getting in the wires would lead me to believe a power wire is touching metal somewhere. Here in colorado we have issues with rodents in the winter time, they like the heat of the engine and they like to chew wires. Other than that, if you want to get rid of the power windows just find some 4runner doors with the crank windows and put um on your truck.
PS: If you do end pulling the door panel, you might want to get some extra plastic clips. You WILL break them. They're 27 years old after all.