This is what I think you need to do. You still currently have the 97 4runner dash harness? Right? So you still have the E12(H) plug. Take that plug, label all the wires, and repin those wires to 99 4runner plugs: E12(D) BLACK and E14(E).
This should basically make the 99 ecu accept your 97 dash harness.
Like i said before. There are two issues as i am not 100% sure. Functions BK and SDL on 97 4runner are no where to be found on 99 4runner ECU. But here is why i think BK and SDL are the same functions as STP and SIL on 99.
Now, let me ask you. Are the big huge plug on 97 ( the one like behind the glove box) the same as the 99? And if i remember correctly, isnt there a small plug next to the big one on the 97?
[MENTION=10169]TheDurk[/MENTION] could maybe confirm that function BK and SDL on 97 is the same as STP and SIL on 99.
And if so, id label everything, and try to repin it and hook it up. So yes, you would have 2 plugs, the rest of the pins on the 97 can just stay where they at. As that plug E12(H) wont go anywhere. I would not cut any wires nor from 97 and nor from the 99 harness. Just unlock the plug, and pull the pins out. Again, label everything, and tripple check it. And do one pin at a time. So if anything you can go back, backtrack your self. So in theory, i think you just need to repin one plug.
Here is a little story from experience on why labeling everything and checking everything over more then once is very important. Especially on a harness, because there are so many wires and some are same color. That is why it is important to repin one at a time. Anyways, my case is different then yours. I repined my auto harness to manual ECU rather then swapping the engine harness. So... i have everything labeled. Just finished repining the auto harness to manual ECU. Plugged the manual ECU, go to crank it over. NOTHING! Freaked out.... went back and reppined the plugs BACK TO AUTO PLUGS lol. I then again, plug back the old AUTO ecu and go to crank it over. NOTHING!!!! Now im really freaking out. Im looking over everything. Remembered that I unplugged the alarm brains. Plug the alarm brains back, and try to start the truck. BOOM it starts. Which means that I reppined it back to the same way it was before successfully lol. Then again, reppined the harness back to manual and was good hahaha.
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