I would recommend adopting Enoch's approach. Although the other solutions will work, and may ultimately produce a bit more power (or a bit less) they are going to cost (possibly a lot) more and take longer.
If one really was looking for the absolute most possible power then one probably wouldn't start with that engine anyway.
Using the original ecu will result in a smooth running reasonably powerful engine, and the only issue to resolve is the manifold. I've driven an indy fitted with the DOHC engine running on the original ecu and manifold and was quite impressed.
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