Brent,
I get a headache at San Jacinto which is under 11,000 ft almost all the time, it just depends on the severity. Under the same acclimitization schedule, I've gotten it so bad that I had to stop every 5 steps while my friend had zero issues. I've had a mild case after spending a week at +9,000 ft.
I have zero issue at the Horseshoe Meadows at 10,000 ft. The point is, as long as I'm not exerting myself, I'm fine. I suspect you will be too. There are people even more sensitive than I am, but I think I'm up there on the AMS-sensitivity scale. I may be short of breath, but am fine otherwise. The level of physical activity is what kicks it in for me.
When you fly, I believe the cabin pressure is set to about 8,000 ft. I'm no doctor, but I think you'll be fine sitting still in a train.
