True, the GEN II (>=04?) loom incorporates a CAN bus, but only between the ECU and the dash. The dash is largely passive in that the ECU just pushes out packets to it (CAN is a broadcast protocol, so there's no acknowledgment from the dash). The exception is the model ID that the dash sends back. The rest of the wiring is 'straightforward' direct wiring between the ECU and the sensor/actuator/switch.lamo, is the engine from an early mille - GEN I or from the later GEN II bike? if its the later bike and you're cutting bits off you may weell have probs as it uses a CAN BUS system so expects to see specific resistances returned. If its the early bike then just look for possible broken wires (you'll need a multi meter for this, not to teach granny to suck eggs you understand ) or a common issue is earthing issues.
Deacs :thumbup