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Is the engine running rough (idle and driving)? If so you could have an ignition system problem e.g. dead spark plug, bad lead or coil etc. You didn't give a lot of information about the problem.
I'm new to the world of HD but I would say either you're running a 2 into 1 exhaust and the side that's not blowing hot air is for looks only or 1 cylinder isn't working.
I haven't messed with my exhaust setup yet but could it be that "feature" that shuts down one cylinder at idle?
No.
Like stated before, stock pipes are a 2 into 1 into 2 design. Most of the gases escape down the straight side, while less amounts make the curves and out the other side. One of those "paths of least resistance". Even then, some of the gases should make it to the other side.
If you're only running one cylinder, it should be extremely easy to tell. 1. Bike won't have much power, be lucky to get up to highway speeds with it. 2. Gas mileage will drop to about 15 miles per gallon, causing you much dismay on any kind of trip. I experienced this back in 1980 on my Low Rider. Fouled rear cylinder plug and didn't know why it ran so crappy until I had it checked. Ran out of gas three times on a 100 mile trip down the turnpike, and was only able to run about 50 mph.
I would guess these newer bikes would act likewise. But it may throw a check engine light (something we didn't have back then).
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