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Yes auto tune will work. The advantage of the after market tuners is greater range of adjustability and options to change the timing.
H-D is limited in the modifications their tuners can go. After the EPA sued H-D and won part of the settlement was no supporting their super tuner and limiting the range of adjustments to ensure they stay within EPA requirements.
Slideshow: From the troubled AMF years to modern misfires, these bikes earned reputations for reliability issues, questionable engineering, or disappointing performance.
Crazy Bunderbike Build Looks Amazing, But Is It Impossible to Ride?
Slideshow: The Swiss custom shop has taken a Harley Softail and stretched it into something so long and low that it looks closer to a rolling sculpture than a conventional motorcycle.
Engraved Rebellion: Inside Bundnerbike's Glam Rock II
Slideshow: A standard cruiser becomes an intricate metal canvas in the hands of a Swiss custom house known for pushing Harley-Davidson platforms far beyond their factory brief.
Slideshow: Harley-Davidson's challenges aren't abstract; they show up in dropping shipments, shrinking dealer traffic, and strategic decisions that aren't yet translating into growth.