As I have stated before I am not a whiz at electrical issues. I went down again and checked my manual on replacing and adjusting the throttle/idle cables and they are pretty specific about the set up. It may not be anything but could the cables not being ohmed out to specks is causing the ECM to shut down the fuel pump? It could be nothing but going back to the initial problem of the cable breaking and the bike shutting down I think I would go back to the start when you replaced the cables and make sure the set up is correct. There are others here that truly understand the electrical system and how or what fail safe may be in place, but if it were me I would be starting from the first issue and making sure that whatever parameters need to be satisfied are met.