The usual culprits are connectors. Most often it's a ground connection in these older vehicles, but the plastic plug-socket connectors can be an issue too.
Grounds to the body can be cleaned and reattached using a new shakeproof lock washer and new hardware if warranted. Just on principle, I would remove, clean and reattach every ground to the body that has any remote connection to the electric windows. If you find a connection that's dodgy, suggest you clean thoroughly with electronics contact cleaner and scrub with a plastic brush. A little bit of dielectric grease in the connector will prevent corrosion. Works for grounds too.
I would also look anywhere the wire can move. Even if the insulation is old and hardened, the wire will not fail unless it is constantly moving, like going from the body into the door.
1990 is not old as far as old car wiring goes. The original wiring should be fine if the Jeep is not falling apart. The wiring diagram in the TSM will show you the presence of any connectors between two points, say at the chassis harness connection and the tailgate. You can test continuity on any of these hidden wires using your multimeter or test light, and another long piece of wire, or a clip lead meant for bridging these far-separated connections.
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If you isolate a break, try running the circuit with the break bypassed with a piece of wire. Then decide whether you will bypass the old wire with a new wire or fish out the old wire and fix it.
Someone donated the electrical section from the 1990 TSM to the Tom Collins site.
https://oljeep.com/gw/elec/GW_wiring-1990.html
Suggest you download all of this, even if you have the printed copy of the 1990 TSM. You can print out the relevant parts of the wiring diagram and trace them with colored pencils or highlighter or whatever as you trace out the connections with your multimeter.