On his blog, XGH often stuggles with God's existence and with the truth of Judaism. Here is comment I wrote to one of his recent posts - I ended up rambling a little:
Seems to me that you struggle with 2 questions and that you need to examine each in a different light:
1) does God exist
2) if god exists, is OJ true?
Or break it down even further:
If God exists, what kind of God is he? Does he consciously rule the world or is all of existence just a sort of "side effect" of God's being? Or does he take an active role?
If he takes an active role, did he actually command us to do all the things that the Torah lists or is that a human document by people who were striving for God?
Even if it's not a totally human document, what level of input was there by God? Written by God, every word? Written by people interpreting the word of God? Written with ruach hakodesh or divine inspiration?
There's a lot behind the question: "Is Orthodox Judaism true?"
Personally, I believe in God (99% of the time - I think 100% is unhealthy to having an active, thinking religion) and I believe in traditional halacha. But what does believing in traditional halacha mean? That all of Torah Sheba'al peh came directly from God at Har Sinai, or that humans extrapolated it from Torah Shebichtav? There are definitely majorly flawed halachot. If it's a partially human system, then you can accept that some of it reflects the biases of those who instituted those laws (and you work within the halachic system to change them). If it's 100% min hashamayim, seems to me that would imply a flawed God. That's why I think that accepting that the system is partially human created invites MORE emunah, not less.