Won't start!

it seems like that everyone that has the click click click wants to try 10 things before testing testing for the problem.
so if you want to start testing her is a couple of things
pull the relay looking at the connector #30 is the ignition power coming in
#85 is the ground coming from the ecu after all the the safety's are met which should be correct or you would not be clicking.
# 86 is positive which should be correct or you would not be clicking.
#87 goes to starter solenoid where you have low voltage .
so i would propose that you make sure it is in neutral (if in gear the bike will take off) make up a fused wire one end to bat positive and other end to relay connector #87 this should make starter crank crank over good. if is on run the bike should start.
if this is working then replace #30 ign wire with the battery fused wire wire
the #30 wire makes a three way connection that corrodes and the resistance drops the voltage going to the starter solenoid the voltage will go down till it drops the woltage on the engine management relay and that kills the ecu voltage after a second the voltage will return and you get another click.
this is why the adding an extra relay works on this type of problem.
now this is not carved into stone but it is worth a try.
 
I put a brand new relay in.
The only reason you would get a click click is low voltage you replace the relay I'm surprised that didn't help still the connector could be dirty Spray it out with contact cleaner and add some Dielectric grease it'sthe easiest 1, Dielectric grease is your friend on the bike connectors get wet and corroded. Second I would clean the start switch and grease or replace third I would clean grease or replace the kill switch. When I bought my bike second hand first thing I did was clean all the connectors and add Dielectric grease I must have forgot that one. All the other switches if they went bad you wouldn't get a low voltage issue you wouldn't get a click click at all. Except for the ignition switch which you said you replaced I think. Good luck, and turbo is right do some tests but I think you said the main ground to the block was good and I think you said you rebuilt the starter so that is why I didn't add that, turbo is much better at this than me, good luck again.
 
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Hate that click click...I have done this fix to 2 of my Rockets & zero problems since.
I tried the other way with the extra relay & it wouldn't work but this way did
One an 06 & other 10 roadster.