I just bought a 90 4Runner, 3.0 manual 4x4, and I started having electrical problems. The first sign was it didn't start after a service at Jiffy Lube, after a couple hours we got it started but there was no specific reason why. I drove it for 30 min and went home. I turned it of and started it a coupe times and it looked good. Then I got out and noticed the e-brake light and the clutch override light was on after I removed the key. Since it was new to me I thought this was a 4runner thing so I waited about an hour researched the issue.
I went out and tried to start it again. The indicator lights were still on and when I tried to start it I lost all power. So the next day I decided to get the battery checked. It was dead and while it was charging I checked all the fuses and grounding points. I heard the grounding on the engine could cause some weird problems so I ran a new wire and beefed it up a little. Then I went through the dash and found what seemed to be remnants of three different stereo system installations. After removing that I cleaned up the battery connectors and installed the charged battery. It started up and drove great. When I parked I opened the door and the interior dome lights didn't come on but the warning indicators were off. I switched the dome light to the door setting and bam, the indicator lights and fan blower kicked on. It was like the key was in the ignition in the acc position, but the key was not in at all.
So I think someone spliced off of the acc wire to fix a broken dome light in the past. Or a harness could be spliced somewhere. Does anyone have other ideas? I plan on going through each harness and checking for splices or ties ins to figure this out. Thanks.

Could also be the leftovers from an aftermarket alarm system.
It's probably going to be a PITA to find.

most def, I also am wondering if it could be the door switch or the relay it is connected to. Do the 4runner's have a time delay when you remove the key and before you open the door? You know where you can roll the windows up or listen to the stereo for a min. Also, it is leaking coolant now. Seriously wondering if I should keep this if it keeps falling apart.

The retained accessory power, (radio and windows work after you turn off the car) is pretty recent. within the last couple years I'd say. I'm wondering if the previous owner wired the ACC to the dome light to mimic that when he wanted. Trace the wires for the dome and see where they go.

Update! I haven't ran down the electrical problem yet, but I got a whole bunch of other things to fix. The water pump started leaking and I have a few cracked hoses. Next I need to replace he timing pulley and idler pulley, the bearings went out. After that I got a general tune up and intake mod planned. The runner will be a beast after all of this.

Well at least you have enough stuff to keep your mind off of the electrical problems

I have a similar issue. My 95 will have low voltage and when I jiggle the wire off the positive terminal to the fuse box viola it powers up. Problem is the connections inside the fuse box look great. Also the motor will completely die due to loss of power and then it will get better. What would cause the motor to lose power and then have power come back on?