Boston recently gave out more than $400,000 in bonuses to teachers and classroom aides at 12 academically struggling schools that showed progress last year, the first rank-and-file educators have been rewarded for boosting the performance of their students. While the amounts are modest, Superintendent Carol R. Johnson hopes the experimental program will evolve into a salary system that can reward all teachers across the city for individual performance, a highly contentious issue with the teachers union.