Look at photos off the original stock exhaust and compare to what you have. or ride it to the dealer and ask them to give you an opinion. The stage 2 you were referring to may have been the headers correct?
The upgrade stages that both the Indian and HD worlds use do not refer to specific products but to areas of upgrade.
Stage 1 is air cleaner and exhaust upgrade. No matter what brand, advertised flow rate etc, you are at stage 1.
Stage 2 is cam upgrade. Once again, any cam upgrade is stage 2. Most people have AC and pipes before cams, and most cam suppliers say you need the extra flow rate of stage 1 to get the benefit of a cam upgrade.
Stage 3 is cylinder upgrade. The Indian 116 Big Bore Kit is stage 3 and because it comes with a dedicated set of cams, those cams are sometimes called stage 3 cams. The forum sometimes has ads for people selling or looking to buy stage 3 cams and it's these Indian 116 kit cams they want.
The stock 116 motor does not have these stage 3 cams from factory. There is a difference between the stock 116 cams and the 116 upgrade kit cams. So even with the bigger bore, it starts at stage zero like the 111 bikes.
Stage 4 is head upgrade, such as custom hi-flow porting, bigger valves, or aftermarket heads. This is not cost effective and not many people chase this level of work. I think Fuel Moto or somebody was developing high performance heads but they discontinued it a year or so ago. I suspect once they got wind of the Challenger they knew there was little value in chasing more power from the Thunder Stroke motor.