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You're right: this is a complicated history. One of the many tragedies within this scandal is that we're not going to get an accounting that answers the famous Watergate questions: What did they know? When did they know it? What did they do about it? Clergy sex abuse clearly did not begin on John Paul II's watch, but the crisis exploded while he was bishop of Rome, and he failed utterly, miserably in dealing with it. We need and deserve an accounting of how and why that happened, and we're not going to get it. The canonization of JPII is a scandal within this scandal. 
Ratzinger was Prefect of the CDF from 1981, but didn't acquire jurisdiction in sex abuse cases until 2001, by which time JP was failing; enter Sodano. But the dossier on Maciel dated to the 1950s, and the accusations against him by members and former members of the Legion of Christ were public in the 1980s. What in the world could have prompted JPII to describe this man as "an efficacious guide to youth"?