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Change in elevation makes the air thinner and should result in richer mixture, not leaner. It may be the quality of the gas or a different blend in that area.
Try running some seafoam through your tank. The ECM should balance out the mixture given time.
EFI has built-in compensation for altitude changes, so the fact your bike was set-up at sea level shouldn't affect how it operates at low altitudes like 2,800ft. Even old fashioned carbs can deal with that change and higher, so it suggests something else is messing you about.
I agree with what the others have stated. Mine was tuned at 700ft and it ran fine at 14,000 2 up when I rode out to CO last month. Gas is only 91 out there but the elevation reduces CCP and richens the fuel air mix.
What others have posted. When tuned at lower altitude, EFI will compensate. Carb not so much. In 1968 had a 428 Grand Prix tuned in Dallas that blew clouds of black exhaust smoke in Estes Park CO.
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