I figured I would post an update just to keep anyone interested up to date. I got my battery tested and it seemed that nothing was wrong with the battery. After looking around the internet at some other people's problems I think I figured out that whoever installed the previous owner's aftermarket radio/DVD receiver most likely did not do it correctly or theres possibly a short somewhere. I unhooked the battery for about 45 minutes (I know I only needed to do it for 15 but I got distracted) and when I hooked it back up everything went back to normal. The clock no longer stays on when I turn the car off and the rear wipers no longer turn on when the car turns off. Like I said it most likely has something to do with the installation of the aftermarket radio but it may also be a bad ignition switch leaving the car in the ACC position. Either way, its okay for now.

I suspect that it's possible your ECU just needed to be reset and disconnecting the battery for a short time period does that, if it were your ignition switch I would think you would still have the same issues.

Haha its funny you say that, I was walking my dog right after I posted this and I realized the same thing. Definitely just needed the ECU reset

Did you resolve the 4Runner issue? I’m having the same identical problem. Any help will be greatly appreciated.

Yep, all I did was reset the ECU by disconnecting the battery for 15 minutes. I'm not one of the experts here so I'm sure there's another way to do that. Hope that helps you!

I am also having the same exact problem with me 2006 SR5. Key fob does not work, ac fan and clock stay on when key is removed as well as rear wiper will occasionally stay on only after key is removed. Already tried disconnecting my battery and putting a new battery in and neither fixed the issue. I presumed it was my ignition switch until the rear wiper started today. Any help is appreciated, really hoping it’s not the body control module.

Try an ECU reset, take off the negative battery terminal, leave it for 15 mins. Should do the trick!

Thanks for the response! I’ve tried that three times with no success. I even left it unhooked over night with no luck.

I'm sad to see this thread died without resolution. I am having the exact same experience when turning my 2007 OFF. Rear wiper runs, key fob doesn't work, all windows remain powered even after opening doors, climate control screen does funny stuff, and I hear the brake accumulator charge up from time to time... All with the key off and removed. Troubleshooting for days. Suspected bad body ECU. OBD2 scanned no problems. Checked fuses, cleaned grounding points, checked suspected wiring harnesses for issues and moisture (been raining alot). Ultimately replaced battery and all went back to normal. Then next morning, after a rainy night, problem is back. Did anyone else find their smoking gun?

Replying to myself here, with a resolution. I discovered an additional odd behavior where all of the electrical issues would go away if I just put my wiper control arm all the way down. Boom, no odd behavior from the keyless entry and everything was functioning tip top. I researched to see how the front wiper controls interfaced with the Body ECU and best I could tell, then don't. So, I was about to start checking for shorts in the driver's kickpanel wire harnesses to see if the wiper controls were sending some weird signal to the ECU, maybe moisture. And that is when I found some dampness, then started following it back and discovered a pretty serious amount of water soaked carpet due to a rear window leak issue (I posted separate on that). So while I didn't find a smoking gun, as soon as I pulled everything up and dried out all of the obvious wet and damp areas, which included the run of wire along the driver's side threshold, everything is back to functioning normally. All I can suspect is dampness causing some unintended voltage signal reaching the body ECU and confusing it. A window leak turns into two weekends lost! Ah well, thanks for being a resource everyone.