Wow, nice family environment you grew up in. A little religious diversity will do wonders for making children side with none-of-the-above. My family was all Catholic, so I never got any of that, but I had a lot of science even before kindergarten.
More specific than the three points you made, just about every area of knowledge we've assembled demonstrates how some part of the Bible was just flat-out made up. I like to look to psychology, myself. If someone is talking to God and hears God talking back, we have medication that will help with that.
I also got a lot of exposure to magic shows, as a kid, so Jesus's miracles just didn't seem as impressive as they otherwise might have.
Please consider joining a group to meet people and talk about anything that's on your mind, Hang With Friends. After you've searched for topics of interest in "Groups" above and in the "Forums", don't forget to look at recent activity which hides along the right margin of the page all the way at the bottom.