sounds like a chain problem. There is not much around that area. If the stress from engine braking is causing it to bind or try and jump a tooth. You would probably feel this in the bike even if just slightly.
How many miles on the bike?
I love my 13. I did a flash, Pipe, Filter, R6 Throttle Tube and R1 shock, damn near perfect. I'm selling a Coffman pipe in for sale if you want to start our with something simple.
Go to your local Cyclegear and but the LED flasher relay for Yamaha. It's on the shelf with all the signals and speedmetal parts. $20 and you just replace the OEM relay.
Simple fix. You can get decent signals as well.