Barfing 2 days before a marathon hike would definitely have an effect on his abilities. But getting to 13K, the altitude likely had a major influence, too.
I would advise you to car-camp at Horseshoe Meadows for two nights before the hike (or one at HM, and the second in the Whitney Portal walk-in sites). Those two nights at elevation will really help the acclimatization.
I hope others will have more suggestions...
