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.

 

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.

 

sounds like it could be a ignition switch or ignition wiring. does it have an alarm on the 4runner? i have an alarm on mine with the auto start and it could send power out when not if system not working right. let us know after u get all the other stuff and if u need help lots of people here to help.

 

Man these 4Runners must be hacker magnets. Mine is doing some weird cutting out when I hit bumps, and the key buzzer is coming on with no key left in so now I cant lock my doors. Under the dash looks like a birds nest. Everything has been spliced and hacked up. There is an old alarm I tried to unplug and then I get some horn in the truck going off. I need some hours with some snips and hope she starts when Im done.

 

I would look in that mess of wires where the steros were hooked up most likely the place.

It would not hurt to get the Toyota electrical manual for your year 4Runner

 

The no start is the ignition switch. Power goes throught the switch rather than a relay. I just hot wired my starter to a PB, simpler that way.

Check the engine, chassis, and battery grounds; something is loose.