For your ECU's I am pretty sure you only have to stick to either turbo or n/a, whether it is auto or manual wont make a difference the only thing, that was mentioned above, would be wiring your reverse lights in. As for the neutral start switch, if you always have the habit of depressing the clutch to start you wont have a problem leaving that wiring bit out, just bypass or "jump" it. I did an auto to manual swap on an 88 turbo and the only thing I had to do wiring wise was the reverse lights, everything else worked just as before. Good luck to you.
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