Typically, an aftermarket exhaust will be tuned for more performance and biased toward making more power up top. The tubing diameter is usually larger than stock, so velocity will fall. If you are looking for mileage you aren't operating in the peak HP range much, so I would expect to see a loss of mileage.
I've added a slip-on muffler to my stock system, and other than sounding better, I don't think it made any difference in mileage one way or the other.
An air filter that flows better most likely won't help mileage much, as the throttle opening is small when cruising and the flow required is minimal.
Biggest gains will come from significant aero improvements.
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