First of all, congratulations on ripping out your immobiliser/alarm. My Honda CBR954RR had one of these fecking Datatool things fitted, one fob and one HISS Key. As complicated as trying to get the Alien out of John Hurt in the movie (programming a spare key wasn't funny either).
All roads leads back to the ignition if that helps. On the 'blade they'd used the relay that cuts the engine if the bike is on its side. A decent meter, soldering iron, heat-shrink insulation and tape will be needed, plus patience and research. Take the battery right out before you start. There's a comprehensive wiring diagram on this site somewhere. I wish you the very best luck!