Although you made some good points Tom, and I do want to address them, I also want to take some time to make sure my answers are well though out. I am therfore going to limit my answer here to one thing you said.
I am curious, since you have read Aquinas, have you read anyone else who talks about they journey of faith? Aquinas was more of a philosopher than anything, and trying to use philosophy to prove religion is worse than trying to use science to do it.
There are a few people who set down to prove that god does not exist and ended up believing. One of them is Lew Wallace, the author of Ben Hur. Another is the British author C. S. Lewis. These men were well educated atheists who wanted to disprove God's ver existance, yet ended up serving Him.
Perhaps their lines of reasoning are not valid for you, but they were for them.