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If one is going to mod their car, I wouldn't suggest getting hung up about those things. Saving money on getting a cleaner car that might be a 99 or 00 would be worth the few hundred bucks to upgrade intakes.
Since he's in CA and wants to keep it SMOG friendly, I'd still recommend a 01 or 02 over a 99 or 2000 of equal condition/mileage/and price. I wouldn't make the model year a priority, just a consideration.
Now as far as handling, F-bodys can be made to handle very good!