How did the speedometer wire get damaged?... Did you raise the bars or get in an accident?
IF you have ever bumped into anything with the front bumper (tree/trailer etc)... check the left side of the overstructure where the front bumper bolts to that... There are all of the brown ground wires tied into that... if the tab for the bumper mount is cracked or broken... you will have a "bad" ground that will cause problems... Or if the bolt has worked loose or there is corrosion on those ring terminals... clean them up.
NOTE: The tab can be cracked but not broken off visually ... check it thoroughly.
Then, with the sled running, using a good quality meter... Check for voltage by back-probing the Red wire coming out of the voltage regulator mounted to the clutch cover (2011/12 models)... and the brown wire connection at the chassis ground... You should have around 14.5 volts.
If it is Not 14.5 volts... Stop the sled ... pull the power-capacitor and check it as follows.
And
Check the ECU capacitor ...
Since you had damage to the hood harness area... disconnect the lighting/charging voltage regulator (so you do don't burn it up... TURN OFF the grip heaters and make sure you don't bump the switch on... best to disconnect the switch.. Then disconnect the hood harness... if your running issues disappear.. you know it is in the hood/gauge harness.
Please note... The lighting/charging Voltage regulator has NOTHING to do with running issues... This is the one mounted to the right side of the of the overstructure next to the ignition coils.
Report back.
I'm having an issue with my 2012 SBA also. Sled seems to run perfectly fine but my headlights flicker from really dim to normal intermittently while riding. In addition, my dash flickers on and off when I stop and let it idle and sometimes will stay off, Tap the throttle and dash stays on no problem.
I tested the voltage reg on top of the clutch cover while running and had no voltage on the orange wire plug.
Brown and red wire plug
6-8VDC at idle, 13-14 at clutch engagement
Yellow wire plug
7-8VAC at idle, 12-13 at clutch engagement
Is this a voltage regulator issue or possible stator? I did not test the other regulator next to the ignition coils. Any help is greatly appreciated!