Here is text of Gary's article:
An FJ55 Rear Window Primer
Few questions appear on the FJ55 mailing list more often than those dealing with rear window mechanism problems. While the mechanics of the lift assembly are relatively straightforward, the electrical circuitry is complicated just enough to be troublesome. Having worked on quite a few 55's with rear window problems I'd like to share some of my experiences with the beast. I'm no expert, just a cruiser owner who has learned a few things through my own experience. My comments are applicable to model years 1970 through 1979, the years I've actually worked on.
Be advised that, as usual, the applicable factory manual for your truck is a great help here. Just having an accurate wiring diagram can be a great help in troubleshooting problems with the rear window. In addition, the steps necessary to remove the mechanism are fairly clearly spelled out in the manual.
The rear window lift/lower mechanism (we'll call it the regulator) works similarly to that in 4Runners and lots of other vehicles. It uses an electric motor with a somewhat flexible coupling to turn a worm gear which drives a plastic toothed gear inside a gearbox whose output gear drives the quadrant gears that make the window go up or down.
I'll try to go through the electrical circuitry first to give a basic understanding of what happens when you try to raise or lower your window. Keep in mind that while I'm no electrician I can hopefully impart some understanding to the reader of what is happening in this circuit. The electric motor has two sets of field windings and three lead wires. The white/black wire supplies the ground for both windings, while up or down movement of the window is achieved by energizing one of the other two wires that go to the motor.
The tailgate must be closed to allow energization of the electrical circuit. This is achieved by "making" the switch located in the upper left (driver side in the US) side tailgate doorjamb. This switch, when made, completes the ground (negative) side of the electrical circuit. In my experience this switch is the most common electrical gremlin, and we'll deal with it a bit later on. The main reason for this switch is to prevent the window from being partially (or fully?) raised while the tailgate is lowered. Obviously, attempting to close the tailgate with the window partially or completed raised can easily break the window and cause lots of damage.
Most 55's have two separate rear window control switches both of which are single pole double throw in configuration. The one on the dashboard is commonly referred to in the manual as the "remote" switch, the other being a key operated switch on the tailgate. Turning either switch to the "UP" position supplies positive current to the blue/white wire of the tailgate motor, while turning the switch to "DOWN" supplies current to the blue/black wire. With tailgate closed and the safety (ground) switch made, working either switch gets positive current to the motor to either raise or lower the window.
Another "safeguard" in the system is the circuit breaker, whose purpose is to "open" its contacts and de-energize the motor circuit if the switches are made for any length of time. Once the contacts in this circuit breaker have opened it usually takes about 10-15 seconds until the breaker cools down and the points close. One more electrical component is the relay. Toyota uses the relay in this circuit to simply allow current to pass through it to the switches through the blue wire. Frankly I don't understand why a relay is used here- maybe someone can offer a bit of insight in this matter. Both the relay and the circuit breaker are located behind the dash.
OK, enough of that. Let's look at some common problems to see what to look for in troubleshooting the window circuit. You insert the key in the tailgate switch to drop the window and nothing happens. You're not happy cause you really want to get your lunch out, and you're embarrassed that once again your window won't work. First thing to do is to listen to hear if the motor is turning while you're holding the switch. If the motor is running and the window isn't working you have a mechanical problem which we'll address later. If the motor isn't working at all, try pushing in on the upper left side of the tailgate to "make" the safety switch a little more surely.
This might be your problem. If so, hold the tailgate in against the switch so you can lower the window, open the gate and see what you can do to eliminate the problem. If the switch just doesn't work you can unbolt it and splice the wires that go to it together. This will give you a permanent ground source, will allow you to raise/lower the window with the tailgate open, and give you the chance to close the tailgate with the window partially raised and break the glass. This isn't really suggested but it's been done many times before. If the window doesn't operate with one switch, try the other- I've seen both failed dash switches and bad key-operated switches.
Another common problem is when the window sticks in mid travel. This is usually indicative that there is a bind somewhere. Misalignment of the lower window tracks with the upper window weather-stripping can cause this, but more often than not tight weather-stripping is the problem. When the window binds it heats up the circuit breaker whose contact points open and de-energize the circuit. Once the circuit breaker cools down (indicated by a noticeable click from behind the dash) the window can be tried again; usually with a helping hand the window can then be raised/lowered all the way. If this happens you'll have to see where the window is binding and do whatever is necessary to eliminate or minimize the bind.
Ok, electrically everything is working. You hit the key, the motor turns and the window doesn't lower. Hmmmm….. Normally in this case the replaceable plastic toothed gear has taken a crap. Very common problem and not that hard to rectify. Here's where an owner can get frustrated; you need to get the mechanism out but can't lower the window because of the problem. Of course you can't get at the mechanism comfortably, either.
At this point you'll need to crawl into the cargo area and remove the cover panel from the inside of the tailgate. It's a good idea to disconnect the negative cable from your battery to prevent unnecessary electrical problems. If your weather-stripping is in poor condition and not sufficiently firm to hold the window up when the mechanism is removed, you'll need to do something to hold the window up. I use two small rubber wedges shoved between the outside of the window and the tailgate.
Having removed the inside tailgate cover, look into the cavity with a good troublelight for the clips that hold the lift/lower mechanism roller channels to the "U" bracket on the bottom of the rear window. I use a large screwdriver to pry each clip out- they are usually (correctly) inserted from the center out and are removed just the opposite. These clips can be tight and one should be careful not to break the ear off the clip when trying to remove it. Once these clips have been removed you can slide the window up away from the two roller channels. This is where you'll need to jam something between the window and tailgate to hold it up out of the way when you remove the mechanism.
Slide the two channels off their respective rollers and get 'em out of the way. It's a good idea to keep everything laid out so later during reassembly you get the parts back in the same position from which they came. Once the window and mechanism have been separated you can usually slide the window down into the tailgate far enough to be able to open the tailgate and allow easier access to the rest of the job.
Once the tailgate has been opened you can slide the window out of the tailgate to get it out of the way. If the weatherstripping on the top of the tailgate is tight and in good condition you'll not be able to remove the window without first removing the "U" channel at the bottom of the window- and this is not recommended. The two weatherstripping pieces can be easily removed to allow removal of the window if need be. Frankly I see no need to remove the window from the tailgate to perform most repairs.
You're now ready to remove the mechanism. To do this, remove the motor wires from the terminal block and remove the four 10MM head bolts that attach the mechanism to the tailgate. The wires are color coded from the factory making things somewhat simple. You'll then need to work the mechanism around, get one arm out and then work the mechanism out through the tailgate access opening. Wasn't that difficult, was it? Once you have the mechanism on your workbench you can apply 12V to the motor terminals to verify that the motor turns but doesn't move the mechanism. If this is the case you'll need to remove the motor and disassemble the gearbox.
The lift/lower mechanism is equipped with two coiled springs that help the motor to "lift" the window. You'll be surprised to discover just how strong these springs are. To prevent injury I heartily recommend using two C clamps or vise grips applied to the frame of the mechanism one on either side of one of the quadrant arms to keep the spring tension from snapping the arms once the motor and gearbox are removed. Doing this also should eliminate the need to "time" the quadrant arms to each other during reassembly. It is also recommended to scribe a line (I use a sharpie pen) across the gears so that, if need be, everything can be easily re-aligned.
To get at the inside of the gearbox remove the nuts that attach the drive end of the motor to the gearbox frame, then remove the straps that cradle the motor and slide it off the gearbox. The coupling may stay on the motor shaft or on the gearbox input shaft, doesn't really matter. Disassembly of the gearbox is straightforward and accomplished by removing the six Phillips head screws from the side that the springs for the arms are located. There are two large screws and four that are smaller. Removing these screws allows you to take off the gearbox cover, and now you can se what the gears look like. Note- there is no need to remove the two large Phillips head screws on the "arm" side of the mechanism- they hold the gearbox housing to the regulator frame and there is usually no need to remove the gearbox from the mechanism.
Replacing the gearset is a simple matter, and it should be quite obvious how to replace either the worm or driven gear. Typically the plastic teeth on the driven gear have been broken; this isn't a great design but it is what it is. Replacement gear sets are available from several sources- I buy mine from Off-Road West but where you get parts is your decision. I use Vaseline to lubricate the gears during assembly although light white grease like Lubriplate might also be a good choice. Reassemble the gearbox using plenty of lubricant, re-install the gearbox and motor and you're almost ready to test. Don't forget to remove the C-clamps of vise grips though, or you might be buying another set of gears! Doesn't hurt at this point to clean off any hardened grease from the quadrant gears and apply some nice fresh Lubriplate to the teeth and friction areas. A drop of oil on all the pivot points won't hurt either.
I test my regulators on the workbench using a spare battery as a power supply. Connect the proper leads and run the lift lower mechanism through its paces. Remember that the ground wire is white/black, the raise positive wire is blue/white, and the lower positive wire is blue/black. Use caution not to run the mechanism to the end of travel in either direction. When satisfied that all is well you can reinstall the mechanism into the tailgate and connect the wires previously disconnected. Slide the mechanism roller U brackets into position on their respective pins, align the slots with those in the window U channel and insert the clips that keep it all together. Sometimes a light tap with a small hammer is necessary to seat the clips all the way. After connecting the battery cable you should be able to lower the window, close the tailgate, and see if everything works correctly. If so, reattach the cover panel and enjoy your truck.
During operation of the window note any areas where it seems to be binding. Do whatever you can to eliminate this problem- I've found that lubricating the channel insides with silicone spray helps a lot.
As an added note let me say there are ways to get around the rear window circuit and make operation simpler. As mentioned earlier, one can join the wires through the tailgate-operated safety switch together and provide full time ground to the motor this way. You can also run a wire from the white/black screw on the tailgate terminal strip to a known good ground. Either method eliminates the need for a functional tailgate safety switch.
When I bought the 72 FJ55 that I use as a trail truck a previous owner had really butchered the wiring behind the dash, including the wiring for the rear window. Not only that, I didn't get a key to operate the tailgate switch. That turned out to be the least of my worries- the key operated switch didn't work anyway. To get the window working in the simplest manner I relocated the dash mounted switch to the outside of the tailgate itself and ran a hot wire to the blue terminal of the switch. Hooked the other two wires up to the correct screws on the terminal strip, and ran a dedicated ground wire to the white/black screw on the terminal strip. My window now works with no problem- no hesitation, no looking for the right key, no safety switches to be made. Obviously security has been compromised but on this truck that's not a problem.
Hopefully this article has shed some light on the mysterious piggy rear window mechanism and will be a help to anyone needing to get his or her window working. I welcome any comments and suggestions that readers might have- we're all just trying to get the most out of our Cruisers. Enjoy those pigs!!!!! Gary Schmauch
It has been a good 10 years since my last repair. 
If I supply power at the the junction block, it works fine. But using the dash switich, nothing!!
