I'd start at the plugs and work your way back. Plugs, plug wire, ignition coil, charging system and battery / battery connections. If all that looks OK you'll need to move onto the fuel system. If it's neither spark or fuel guess you might do a compression / leak down test on the rear cylinder. My cousin rides a 2011 HD and he was having a very similar issue. Seemed like the rear cylinder was miss-firing. We changed plugs, replaced the rear plug wire, checked fire from the coil and then went through the fuel system. We didn't check the battery because it was less than 2 months old. Problem persisted. Travis called me a couple of days later and said his bike was dead in the parking lot of the gym and that he needed a jump or a tow.
I got on the road and about 20 minutes later he called and said that he had a loose terminal on his battery. He tightened that up and hasn't had an issue since.
Maybe you'll get luckly...................
The last thing I can think of is that maybe the rear cylinder O2 sensor is acting up.
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Last edited by wevsspot; 09-28-2017 at 02:39 PM.