Three hours before her 8 a.m. classes begin, senior Mya Shiloh is already on her way to San Jose’s Lincoln High, nestled into her favorite seat on the morning’s first ACE commuter train and trying to grab a few winks after waking up at 4 a.m. at her home in Tracy.She’ll be back on the train by 3:30 p.m., and home more than 12 hours after she left. Her schedule cuts into activities she loves, like school clubs and drama, as well as socializing and sleep — but it’s the price she’s chosen to pay to stay in her beloved high school after rent hikes priced her family out of San Jose.Mya, 17, is among thousands of school children who have been uprooted by the Bay Area’s high housing costs, and one of a small but growing number who embark on long daily commutes this month as they go back to school.A tight and astronomically expensive housing market is forcing families to face wrenching choices: to uproot, make marathon drives or cram together. But the market is also reshaping the size and makeup of some Bay Area schools, as displaced families leave and re-enroll their children elsewhere.In the San Mateo-Foster City School District, for example, enrollment grew last year despite the loss of 500 low-income students who left the area, said Assistant Superintendent Donna Lewis.