Jay, I can understand your concern. In the end, we can ask all day long, "Why would THAT shake your faith?" but in the end, it doesn't matter. What matters is that it did. So, how can we fix it?
First, let's start with the idea that all the NDE's, as nice as they sound, are just nice stories. Some are very convincing, but I would encourage you to google "Near Death Experiences" and see what happens. There are pages that are devoted specifically to the stories of people who have had them. Now, I don't read the accounts and say they all lie. In fact, I believe most of what people have written on the issue, so far as personal experience goes. But, what you will find is that there are so many conflicting accounts, that the obvious conclusion is that what people experienced is not objective reality, but rather something subjective. It happened to them because of the way they are wired. In other words, if people claim they went to heaven, they really didn't. They had an experience that they thought was heaven. Probably, that experience was nothing more than neurons firing off in their brain and exciting certain preconceived notions . . . it's very much like a dream. Have you ever been studying hard for a test ALL DAY LONG, and then you go to sleep dreaming about the subject? I wouldn't say that NDE's are all that different. Of course, that doesn't mean people will always have one. After all, you don't always dream about the test when you've been studying for it, do you?
So a little research into NDE's can calm your concerns there, but what about proactive approaches? I can tell you that there are certain things that I don't understand, but they don't challenge my faith anymore. The reason is that I can't stop believing if I want to. I did a very serious study on the Resurrection accounts of Jesus Christ, and unless I decide to make some wild assumptions, basic logic tells me that He HAD to have risen from the dead. Now, despite what people may say, if Jesus rose from the dead, Christianity is true!
I would recommend getting into some basic apologetics. Start with the easy stuff. C. S. Lewis'
Mere Christianity and Lee Strobel's
The Case for Christ are probably the easiest readings and clearest explanations of two approaches to a rational defense of the Christian faith. Then, start working your way up. You'll find in no time that Christianity is rational, and to be honest, it is the only world view that makes sense. Everything else is just idiotic--no exageration intended.
God bless
Oh, and one more thing: James 1:5-8 saysm "If any of you lacks wisdom, he should ask God, who gives generously to all without finding fault, and it will be given to him. But when he asks, he must believe and not doubt, because he who doubts is like a wave of the sea, blown and tossed by the wind. That man should not think he will receive anything from the Lord; he is a double-minded man, unstable in all he does." If you have questions, go to God. Ask Him to show you Himself, and He will . . . Bible promises so