I have a 96 CBR600 F3 with 32,000 miles on it. I took a 800 mile weekend trip a month ago(By myself and 100s of miles from anyone I knew). Which I went from Atlanta, GA to Augusta Georgia in which you go down in elevation. Then I rode from Augusta to Deal's Gap and ran the dragon in the same day. Then the Cherohola (which does reach over a mile at one point) the next day and back to Atlanta including riding in rain the entire way back.
Infact here it the route from Augusta to Deal's Gap that I took...
http://maps.google.com/maps?f=d&hl=e...108643&t=p&z=8
I didn't notice any problems with the bike nor a performance loss(even with my carbs tuned for Full exhaust and having stock exhaust on it). I felt like the exhaust got quieter when I went in up in elevation fast but my friends with their EFI bikes(Not at the gap but another mountain) noticed teh same thing with theirs.
Of course comparing my mountains to your mountains would be like comparing Paris Hilton's breasts to Dolly Parton's breasts. You just can't.
I think your bike would be fine but maybe do some test runs up a very tall mountain to see how it really feels. Also my buddy's GF just got a brand new ZZR600 and those things are freaking sweet. Even though they are carbed.