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Well in 01 IIRC they switched to PI motors so their is a gain by switching them. Other than the bigger alternator if their the same exact motor as the Grand Marquis the plenum/airbox goes toward the drivers side instead of the passangers side.
No, the alternator is bigger so it can provide the energy required to run all of the electronics found inside an interceptor. It wouldn't be worth it, they arent hot rod engines like everyone thinks. Although if you ever stumble across the DOHC 4.6 out of a Maruader, ****** it the hell up.