Although it was long, long time ago when I had my crisis of faith, I do remember that the basis of it was exactly the same as yours - I didn't think that many of the teachings of the Catholic Church about what was moral and immoral agreed with my personal thoughts, and more importantly, made much sense. Many of them seemed more like traps to ensure that everyone had something to confess rather than reasonable guidelines for how you should act.
Many Catholics just ignore the dogma that they disagree with; I know of many in my own extended family who practice birth control and don't care what the Church thinks of their actions, despite still going to church and professing Catholicism. Personally I think that's hypocritical, and I prefer your stance where it is more of a struggle between doing what you think is right and what the Church tells you is right. I would strongly encourage you to look at finding a religion (or lack of religion) that agrees with your personal principles rather than fitting your principles to your religion; you don't have to be a Catholic to be a Christian, if that is still your choice. The guilt is merely an admirable reaction to this conflict between authority and your conscience - change or abolish the authority, and the guilt will go away.
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Better educated sadness than oblivious joy.
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