1) Listen to our class from several months ago, "Marranos, Responsa and 'Jewishness'" here. Follow along with the sources here.
2) Read the full text of Maharit Sahalon here. Read the full text of Yosef Hayim Yerushalmi's analysis in From Spanish Court to Italian Ghetto here.
3) Several years ago, Yerushalmi's student David N. Myers wrote a wonderful piece for Tablet on Yerushalmi's life accomplishments in the field of Jewish history, entitled "Freud and the Marranos: How Yosef H. Yerushalmi Gave Voice to Jews Caught Between Worlds." Read it here.
4) Prof. Israel Ta-Shma pieced together a summary of the various relevant issues that were treated in teshuvot with regards to Marranos, entitled Ma'amad HaAnusim LeOr HaHalakhah. Read it here.