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What are your goals for the car? The best 1K you spend on a drag racer won't nessacarily be the best 1K spent on an autocrosser or road racer or a show car...
Get the CAI and Tune. You can feel the increase in performance in the seat of your pants. Plus, your mpg will increase. I did mufflers first because it was the cheapest thing I could do for the money I had at the time. Lethal Performance has Pypes muffler at a discount for forum members. They are sponsors on this forum. Contact Jared.