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I just put an AFE intake on my 2009 V10. I prefer to call them "open element" intakes as I feel the stock intake brings in colder air. I did the tuner and exhaust all at the same time so I cant offer any info on just the intake mod. I added the outerwares cover on it as well.
Your 2006 V-10 should not need a new Y pipe as it is a 3valve with an improved Y pipe design. I added an Airaid intake system, Magnaflow exhaust and a Mike's 5 Star, mostly in the 89 octane performance/ tow setting. I'm not much of a Zoodad fan for the gas engines, since it is most effective on turbo diesels.