DandyDan - if you are following a religious tradition that allows you to take what works for you and ditch what doesn't then i don't see any reason for conflict. Some churches are liberal, others are not. If your tradition requires specific beliefs and you don't honestly believe them then i would question why you would identify with that particular faith. You could be rc and not accept all the edicts of the catholic church, re contraception for example, but i would still think there is a bottom line where if your beliefs diverge substantially from your chosen church you should really examine why you are still a member.
Regarding prayer, if i believed in an interventionist god who could do miracles and answer prayers, i would expect him to cure small children when they are dying, especially when thousands are praying for them. The fact that he does not would make me question whether there is a god that intervenes. That would make more sense surely than saying it's not gods fault, we just have to trust he has a plan, it's because this is not heaven - no, but it is still his creation (if you believe that), and so is responsible for everything he created in it.