Bridge-rectifier motor surge clamp...
So here is a copy of the Toyota wiring diagram of the power window circuits on the FJ80:
And here is a section showing just one motor and switch with the bridge-rectifier spike clamp installed:
The ring of four diodes connected in this fashion is known as a "bridge rectifier," or a "full-wave bridge rectifier." These are available in small four wire packages which are very easy to use for this application. You don't need an great amount of current handling, because it is a very brief spike, so a small package should be adequate. These will normally be capable of handling a couple hundred volts without damage. Available at any good electronic component shop, or mail order from somebody like digikey. Should be cheap.
To expand on the earlier description, now that I've got an illustration: If the motor generates a positive spike that is higher voltage than the 12V battery voltage plus 0.7V to turn on the diode, then one of the upper diodes will conduct the current to the battery, if the motor generates a negative going spike more negative than ground by 0.7V, one of the lower diodes will conduct the current to chassis ground (effectively back into the negative terminal of the battery). The bridge rectifier has no effect on any voltage across the motor that is battery voltage or less, meaning it has no effect on the normal powering of the motor. It will only cut in for a few milliseconds during a high voltage inductive spike generated by the collapsing magnetic field in the motor when the window switch is opened, but that is the spike that causes the arcing on the window switches.
I guess one other comment is in order. For this to be fully effective, it is important that the door chassis is well grounded back to the battery negative terminal. I haven't measured that on my rig yet, but will be doing so. If you get more than an ohm or so, you probably ought to add a bonding wire that ties a ring terminal to a screw in the door back to one of the grounding points in the main chassis. This isn't needed by the motor drive because both wires for the motor go all the way back to the main control panel in the driver's door, but the ground is necessary for the spike clamp bonding to work.
I've got one door motor done, but as I do the next installation, I will take some pictures to show the installation.