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idle speed - either too high or too low I would imagine the changes you made somehow altered the engine idle speed. I know when my idle speed was too low according to the service specs that I had hardly any horn movement. When I got it into the recomended range, the horn and bars bounce like I like them too. As soon as you roll the throttle on, she calms right down.
I would check the front motor mount...a bad one will make for excessive vibration.
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You may want to consider upgrading from the stock handlebar riser bushings to polyurthane. Harley and the aftermarket has these available. These do make a considerable improvement over stock.
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If the vibration is mainly in the fairing....remove the fairing and you might have broken brackets(s).
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I would rule the above out before going any further. I do not suggest or advise adjusting the RPM to any other than what is specified in the OEM shop manual. Too low of an idle...and you're just begging for problems.
I don't think it a broken fairing bracket but it does feel as if the motor is hard mounted to the frame \\; The first thing that came to mind was the motor mount \\; I don't know if they had to take it loose to install the pipes or not?
the rpms are the same as before she just shakes ALOT more than it did!!
Had the same issue on mine. If you notice, the crossover pipe you removed served as an exhaust flow and also a support brace for the rear of the engine. \\;\\\\\\; It tied into your right side pipe and that mounting bracket hooked to the frame right below that. Crossover gone = less support = more vibration at idle. \\; No fix that I'm aware of. \\; I do notice people looking at it shake at stoplights though.
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