If its the aux circut the runs the passing lamps that's dead then you might have recived an a new but older generation
dyna 3000
ign box that you had to do wiring mods on to get the passing lamp/aux light to work with.
It was either 03 or 04 & newer R* that this is an issue with when it comes to the older not revised dyna 3000 ign boxes that were from that i understand revised in mid to late 2009 so there can be older but still new non revised ign boxes still out there.
If this seems to be your problem there is a simple wiring mod fix thats avail from dyna to fix it so go to thier website to get their tech phone # & call them for help.
I believe if you look hard enough you can find that wiring mod someplace on their site .
Update:heres something i had saved on that issue i mentioned above.
Dynatek D3K73, Dyna 3000 Ignition System for RoadStar 1600/1700
Note, Will NOT work with 05+ models with factory installed driving lamps. Custom wiring will need to be done, see Dynateks website for more information.
SALES SUPPORT: For any sales related questions, please contact us toll free at the following telephone numbers:
Dynatek Products (Dynatek Ignitions, Accessories, FI Controllers, Etc...): 1-800-928-3962
Scott