Check out the FAQ area on the Nology site about timing issues. They seem to suggest that a little timing tweaking might be needed. DOH!:

Nology Hot Wires FAQ

Do we have resistor or non-resistor type plugs? What kind of ignition system do we have?

-CT 2003 Speedmaster - 125/42, 17T Sprocket, AI Removed, K&N 2006 Speed Triple 1050