To my knowledge the Thunderheart controller is for Harley Controls only (Positive voltage/higher amprage). The 2004 and up BDM hand controls run of a negative control unlike HD and are made to only handle very low negative current.. The controls are all curcuit board, low voltage output and you may need to buy the Wire-Plus module to make the hand controls happen. The problem you are going to run into is needing to have a bank of relays to handle the current of the headlight, the horn, the start button, and then changing the brake switch from negative to positive to match your rear brake switch. In order to change the brake switch from negative, the curcuit board will need to be removed and a trace cut and a jumper wire soldered in to on of the wires from the run button.
That Thunder-Heart controller really is going to cause you a lot of head aches and a big mess of wiring up relays to do it. Trust Me !!!