I haven't read a ton of Japanese SciFi however I have heard good things about the Galactic Heroes series. I have a friend who travels to Japan a few times a year for work and is big into SciFi, I'll have to ask him for some recommendations and get back to you.
As for Holy Cross, you do recall correct, they are indeed a Jesuit school. Honestly I'm not the best person to ask in regards to Catholic subgroups. I do know a small amount of the history; basically the Jesuits are a Liberal Catholic offshoot from France that thought spreading education was the best way to serve God, so their missionaries built schools and the like. I am actually an atheist and was attracted to Holy Cross because they have one of the best Linguistics programs in the world (Look up Claudia Ross sometime if you are interested in Linguistics, she is the head of the Linguistics and Language departments at Holy Cross, she is nothing short of brilliant) rather than the religious side of it. From a practical standpoint, the only way that the school being Jesuit effected me was that I was required to take a semester of a religion class as one of my common requirements. I took "Ancient and Medieval Hinduism", because, well, why not? It seemed interesting and while I particularly disliked the professor the material itself was indeed quite interesting.