Of course. Wasn't thinking when I read that.
This still doesnt sound right. Let me look at mine this evening. I have a manual ECU from both a 4runner and a Tacoma. I am almost positive that both have 3 rows of pins.
Where did you get the ECU from? Is this the one out of the 1996? I have a hard time believing that it has something to do with the limited trim level, but I could be wrong. It more than likely has to do with the model year, 1996.
Ah - if you still have the manual shift, I would recommend putting that in as much of a pain as that might be. Those electric shift cases rely on a solenoid to engage. More electric items to screw up. If you keep the electric case, you may check over on ttora for some threads on the matter. Those cases were fairly common in Tacomas as well, and I think I read a thread or two on it back when I did my swap.