The stock exhaust header is really a 2-1 system and yes a 2-1 pipe will perform better. The crossover pipe is for reverberation only. This is so the exhaust sounds the same out of both pipes, while the right pipe has most of the exhaust gases. You can feel the left pipe is cooler than the right and on a cool morning will even see more condensation coming out of the right than the left. It is important for performance that when you consider slip on mufflers you should ask about the baffles installed. On Fuelmoto mufflers Jamie puts a larger baffle on the right and smaller on the left for a reason.

 

Yeah, the the stock is exhaust is essentially a 2:1 with the left can being mostly for show. When I put V&H ovals on my stock headers, I noticed the inner oval tips were aging (discoloring) differently because of the heat/exhaust difference between the two sides. I finally settled on True Duals with V&H Classics and the bike/engine and my legs are much happier.

 

HD is not worried about getting performance out of the stock bike! If they were a 96" engine would be coming stock with 100HP / 100 Tq stock like it should. Instead they know we'll spend a fortune building / tunning it up to where it should have been in the first place. This subject gets me fired up.