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As long as you take the SH engine, tranny, ECU, harness, and intermediate shafts and install them on the base chassis, you should be ready to go.
However, if you're going to do this, it will be easier to do the following:
take the engine from the SH, and fab the tranny from the base model to fit the SH block. That way you'll be getting the benefit of the SH motor without the hassle of ATTS. Also, you won't have to swap the intermediate shafts. I think if you do this, and use your base ECU and harness, you'll be in good shape.
This would basically be a SH->base swap, but doing it in a base chassis instead of an SH chassis. See what the SH->base guys did, and do that to your SH block and put it into your base chassis; I guess is what I'm saying.
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Type-S Swap.
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