Even CNN notes that this claim is simply an allegation that's bandied about. Pope Pius IX was hardly an advocate of putting Jews in ghettos since he was the one who abolished ghettos in Rome.
"It seems clear from the historical record, in fact, that Pius had no hatred of Jews. Upon his election in 1846, he was hailed by Jews as their best friend in Italy. In 1847, Mose Israel Kazzan, Chief Rabbi at the Israeli University in Rome, dedicated a psalm and prayer to the "glorious and immortal" Pope....
"On the night of April 17-18, 1848, Pius IX ordered that the doors of the Jewish ghetto be knocked down. He abrogated the undignified and humilating tasks the Jews were forced to carry out. He declared that "they were not foreigners," and had their streets patrolled to pretect them from a popular uprising that had broken out aginst the ghetto's emancipation."
http://www.geocities.com/orthopapism/piusix.html
As for your quote from Pope John XXII,
"I was recently told that according to Dr. Eugene Fisher, expert on Jewish-Christian relations with the U.S. Catholic Bishops' Conference, this prayer is not authentic. ... Please, add this disclaimer if you want to cite the prayer. From the Jerusalem Post, Internet Edition"
http://ecumene.org/SHOAH/shalom.htm
Here's another clue. Vatican II overturned no doctrine. Doctrine is synonymous with catechesis. The Catholic catechism has never taught that the Jewish people are responsible for Christ's death.