What should I spend my next few years of rationalism doing then?
It seems that according to you, my options are
a) leave my religion in favor of rationalism. (feel free to tell me this, but if my parents find out about it they'll be worried and start telling me you're a satanic cult. I can handle it.)
b) leave rationalism in favor of religion. (not likely. I could leave Less Wrong if it's not open-minded enough, but I won't renounce rational thinking.)
c) learn to live with the conflict in my mind.
Suggestions?
These are not "options", but possible outcomes. You shouldn't decide to work on reaching a particular conclusion, that would filter the arguments you encounter. Ignore these whole "religion" and "rationality" abstractions, work on figuring out more specific questions that you can understand reliably.
If it's worth saying, but not worth its own post (even in Discussion), then it goes here.