Well it's because once you hit 42, the main plot EXP rewarded levels you to 43 (which is where most of that gap comes from). The question is, how did he reach 42 with less exp from World Boss, while you're still at roughly 40%?
My only conclusion then would be aside from buying stamina, he must have also cleared higher levels of Ninja Exam than you did, and has been continually sweeping higher than you as well.