If you have a new ECM you have lost your S&S download. You will either need to get another download (I assume your download card is gone) or you need to get a fuel controller of some sort. It will be very lean with the stock download and your airbox and pipes.
2006 Victory Kingpin
110 Cubic Inches -- Balanced S&S crank/rods, Lloydz iron liner big bore, 11:1 Wiseco pistons, massaged
stock heads, stock throttle bodies/injectors/intakes, S&S .495 cams/springs/retainers, Torque Tubes
airbox, RPW Thor pipe, Lloydz ECU, PC-III, Rivera Pro clutch spring, 31 tooth pulley w/Buell belt