my uncles 85 runner had the same problem
ended up he was leaking from the antenna hole (where the antenna cable goes thru, out the cab and up the fender)
we sealed the antenna mount at the fender but it was still leaking thru
well it was the same hole that it was coming thru but we noticed that when it rains hard enough the vents on the front top of the cab (where the bottom of the windshield is) would fill up and overflow (Dont know why it wouldnt drain) and the water would come down the antenna cable coming inside into the cab
you couldnt see where it was comin from and it would just puddle
well it came down right next to the ecu on the passenger side, with rubber/plastics removed from that area you can see it flow like a creek lol
we didnt/couldnt fix it, i told him just make sure to remember to pull the drain plug on the floor when it rains
