If you are going Happy Isles to Whitney, and concerned about acclimation, take the first leg of the trip slowly. Consider spending a night at Little Yosemite, doing the side trip to whichever (Half Dome or Clouds Rest - the view from the latter is better, and considerably less crowded) and spending another night along the trail to Tuolumne Meadows (Sunrise or Cathedral Lakes) then a third at Tuolumne. TM is at 9,000 feet. If at any point along this leg you feel symptoms you could opt to lengthen the time at TM another night to see if you feel better. If you're okay, move on down the trail. If symptoms don't abate you have a decision to make and can hop on the hiker bus back to the valley if you decide to bail. Coming from Happy Isles is actually a pretty good acclimation curve. Easy to go slow when things are that scenic.

You'll probably feel it more in the first week than in the last - which will be good, by the time you get to the last leg of the trail, hitting a pass every day like clockwork will be no sweat.