I'm running my 2006 with Vmod stock pipes and K&N. PC3 and a map from the Dynojet website works great. Good power and fantastic sound. The Vmod stock mufflers sound the best in my opinion.
Your ECU flash should be pretty close. Swap them out and see if it feels right.
Both should run equally well, no difference in power between them. The VMOD will be louder and sound harsher, the screaming eagle will be deeper and rumble a bit more - especially if its the version with a central plug that's been punched/drilled out.
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