Hi Adam,
It's Joe. No, the LH side is definitely not stock. On the top of the top muffler on the RH side (brake lever side) you will find the code HM460A; that is the OEM exhaust part code.
If you are having problems with just one of the 2 cylinders running off that particular 2 into 2, it's probably not exhaust-related. Afterfires can be caused by a host of reasons but usually it's caused by unburned fuel lighting off when it hits the hot header pipe on the exhaust stroke. So, perhaps you have a weak spark in the cylinder. I would start by warming the bike up and spraying each header pipe with water; is #2 noticeably cooler than the others? If so, it most likely is a bad coil, plug wire, or spark plug (or any combination thereof). There are other possibilities but these are the most common culprits. Hope this helps.