First off, clean your air filter!
I live in Sacramento and do most my riding there. That is about 100 feet elevation. Really nothing. I also head up into Nevada where I ride at about 3000 feet. I was running a CRBM and 2Bro full exhaust and it ran pretty good. I think it actually ran stronger in Nevada. It poped a bit in Sac.
Hmmm... I forgot my point!
With my YFZ I tried rejetting for different elevations but it always seemed that the normal set up I ran in Sac was good for Glamis, Pismo, and Nevada.
Oh! I would would tune for the lower elevation unless you have the ability to get accurate A/F readings for both elevations. Then you could set up 2 different maps.
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