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So my issue started after letting my bike sit for about a year. Every month I’d drive it around the block to keep the battery charged, but no further. Last week, after trying to start, the bike wouldn’t budge. The starter would click, fuel pump would prime and engine would crank but it still didn’t start. On top of that, the headlights and horn stopped working as well, which I’m pretty sure happened at the same time, so they’re related. I’ve tried changing the spark plugs and cleaning the fuel injectors, but still no luck. If any mechanics know what could be wrong, please let me know, any help is appreciated. Thanks!

Also, I changed out the battery already so it’s not that.

My bike is 2015 Yamaha R3.
 

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I'd check with a multimeter that the new battery actually has the charge first.

Check the table below which I borrowed from Revzilla article for the numbers:

VoltageState of Charge/What to do
12.73 or better100 percent. Go ride.
12.62 90 percent. Charge it, then go ride.
12.50 80 percent. Charge it, then go ride.
12.32 70 percent. Charge it, then go ride.
12.20 60 percent. Charge it, then go ride.
12.06 50 percent. Charge it, then go ride.
11.90 40 percent. Try charging it, but it might be toast.
11.75 30 percent. Try charging it, but it might be toast.
11.58 20 percent. Battery has converted to doorstop.
11.31 10 percent. Battery has morphed into boat anchor.
10.50 No meaningful charge. Check to see if battery has been replaced with rock.

Also, are you sure there was no short circuit prior to when the horn and lights stopped working? Could the fuse blow for any reason?
 

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Riding around the block probably isn't enough to recharge the battery all the way. Might even damage the battery if you were already low on battery life. I'd recommend hooking it up to a trickle charger instead. Or at least ride it for a good 30 minutes.
 

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Do you know if the Ignition Switch recall fix was performed for your motorcycle?
You may be able to check by inputting your VIN on NHSTA Vin Check

Recall No. 17V112000
Report Receipt Date: Feb 21, 2017
Component(s): ELECTRICAL SYSTEM:IGNITION:SWITCH

SUMMARY
Yamaha Motor Corporation, USA (Yamaha) is recalling certain 2015-2016 Yamaha YZF-R3 motorcycles. Water can enter and corrode the ignition switch resulting in an unexpected engine stall.

CONSEQUENCE
An engine stall increases the risk of a crash.

REMEDY
Yamaha will notify owners, and dealers will replace the ignition switch subassembly, free of charge. The recall began March 9, 2017. Owners may contact Yamaha customer service at 1-800-962-7926. Yamaha's number for this recall is 990112.

NOTES
Owners may also contact the National Highway Traffic Safety Administration Vehicle Safety Hotline at 1-888-327-4236 (TTY 1-800-424-9153), or go to www.safercar.gov.
Source

Idea ripped from this post (Thank you, @BluebirdR3)
 
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