Not Ranked
The Gen III engine is the best, with the possible exception of the intake.
The best combo would be the Gen III engine with the old (red, dual throttle body) intake.
The new intake was designed to fit under the lower hood. The old intake will flow better and support the better breathing heads. I do not know what, if any changes (most likely non) might be needed in the computer if you swap intakes (not all that expensive, they go for $200 or so on ebay fairly regularly...just make sure you get the fuel rails and injectors...the injectors are unbelievably expensive if you try to buy/replace them through 'ordinary' channels).
What happened to the trans?
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