I have a sand rail that had a 2000 R-1 in it and I did a simple engine change to a 2004 R-1 so I though. I?m on week three trying to get this thing running. This is what I have so far, the wire harness has been cut down (IE) all lights horn, signaling, fan, fuel pump, fuel level, I?m running a after market one. I could not get power to the start wire blue/white so I put the key switch in now I have power to the start system. The engine will turn over now but I do not have power to the fuel injectors. This is what I have done to the wire harness so far. 1) SIDE STAND SWITCH blue/black wire to ground diagnostic shows it good. 2) CLUTCH SWITCH blue/yellow and black/yellow are hooked together. 3) NEUTRAL SWITCH I know this is good because the dash shows it working. 4) STOP SWITCH red/white and red/black are hooked up in a switch in the car. 5) MAIN SWITCH like I said I put the key switch in. 6) START SWITCH this is hooked to a switch in the car. 7) AIR INDUCTION SYSTEM is removed and block-off plates installed. 8) LEAN ANGLE SENSOR is working. The fuel pump is not hooked up because I?m running an after market one and the fuel warning is not hook up. I do have spark to the plugs now and all the other sensors are hooked up. I do have a service manual and been talking to my Yamaha dealer and they don?t know what?s going on. I have 2EA. STARTING CIRCUIT CUT-OFF RELAY and tried both of them with the same thing. The red wire coming out of the starter relay has power going down to the cut-off/ fuel really I can hear the relay click but I'm not getting power out to the red/blue wire I have two cut-orr relay's and both do the same thing. Did a diagnostic and I'm getting an 11 code. It doesn?t show up on the dash intell you go to the diagnostic mode and I think it's in the malfunction history. I cannot get it to go away and this code's out to the cylinder identification sensor. This code will make the motor unable to start but I do not know if it?s an old code from me messing it the first time. I do not know how to clear the code and do not know if this code is in the ECU and will cause this to not get power to my FI.