This thing was in the driver side kick panel, no idea what it is, but it doesn't look factory to me.

http://imgur.com/a/Zi0o7

Edit:
Out of an 88 4Runner DLX, 22RE, manual

 

Servo motor controller. Definitely not stock.

 

After market cruise control box.

 

Ah ok, that makes sense.

Did Toyota have a factory option for cruise control for 88 runners?

 

I am pretty sure I pulled them off my 87 4Runner so I am sure it was a option.

 

I does look like an aftermarket cruise control or security system. Some trucks did come from the factory with cruise control. In front of the clutch master cylinder is where the vacuum tank sits if it is still there, on the speedometer bezel would be some buttons, drivers kick panel is a brown (if I recall right) box, that are signs of the factory cruise control.