Does it run on both cyls or just one with that code?
Ron
engine light and code p0261
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Also does the bike have an aftermarket exhaust and possibly a hidden piggyback fuel tuner box or a re-flashed ECU ? If so unplug the tuner, let the ECU revert to the H-D OEM fuel calibrations and ride it see if the code goes away, might not happen immediately but it could. Also remove, inspect, clean both sides of ECU wiring plug and check back side of plug pins for moisture & corrosion whether it has a tuner or not. If all that plus prior suggestions here does not make the code go away ride it and watch it - if rear cylinder is not overheating, popping or running real rich and fuel mileage is about right 30 - 38 mpg in mixed riding don't worry about it - ride it until the code goes out or if it really bothers you buy another ECU but that's big bucks ! Also as a final test swap injectors see if code goes to front cylinder. If non OEM injectors they can be bad right outta the box, so you can vindicate with science by swapping them - Best of Luck with it ! 
julian.aubourg - I Got it, may be in ECU - Bottom line is when you ride it what happens other than the engine light is on & a code ? Does it ride out & run OK ? Idle OK ? Hit 8999 rpm OK ? Have you ridden it any distance at all with the light on ? Reason I ask is I see this all the time with jets - there's actually nothing wrong with the actual system but the monitoring system has a problem and it's telling you the actual system has a problem when it actually does not.
At the end of the day if it runs out OK with the light on I'd ride it and watch it, carefully. Eventually it may regain it's composure and the light and code may go out. It's all about your tolerance for having the light on while you're riding it if it actually runs well. I've had the SES light on in a vehicle that I replaced the all the fuel injectors on for hundreds of miles then one day the light goes out and never comes back on - it's like the ECU felt obligated to tell me there was still a problem when actually there was not - slow memory dump, slow to realize the problem was cleared, whatever - just saying - Best of luck with it -
At the end of the day if it runs out OK with the light on I'd ride it and watch it, carefully. Eventually it may regain it's composure and the light and code may go out. It's all about your tolerance for having the light on while you're riding it if it actually runs well. I've had the SES light on in a vehicle that I replaced the all the fuel injectors on for hundreds of miles then one day the light goes out and never comes back on - it's like the ECU felt obligated to tell me there was still a problem when actually there was not - slow memory dump, slow to realize the problem was cleared, whatever - just saying - Best of luck with it -
Kind of - I'm a corporate / private jet mechanic, I don't own them but the planes are my babies ! Yes it was a GM S10 SUV that had the stuck SES light - and our V Rod EFI ECM is a Delphi, GM product - co-incidence ? I think not -
Compare voltage at the system relay and each injector, key on in this pic. Should be identical.
Unplug the ECM and pop the plug cover to access pin numbers. Resistance between 19 at the ECM plug and injector #3 and ECM pin 21 and injector #2 should be the same.
Ron
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