I won't be the last word here, but just wanted to relay my experience with my all stock 94. I did a cross country this last September and went from Ohio to Oregon and California crossing several mountain ranges at 5-7000ft. I had no noticeable issue except on first cold start in the morning. The only time it got doggy was a 10k pass near Vale, CO on the way home.

 

If the carbs are out of the bike, I'd bump them up to make up for the factory lean condition and ethanol in the fuel. Other than that, as cb2cbr says, shouldn't be a problem at altitude.