I was on my first playthrough on hardcoe mode, and i was talking to Waking Cloud about her beliefs, and I am confused. She has the Randall Clark, aka the survivalist, confused with God from the bible, correct?

Yes, and you can point this out to Daniel.

Well, not exactly. see Daniel is trying to convert them to Christianity while they use to worship "the father in the cave" that thought them to be kind to others, violence is a bad thing. they saw the similarities and kinda combine the two together. at least that's what i think.

The Sorrows have always worshiped Clark as their deity. When Daniel showed up talking about "God the Father" who will bestow blessings upon the chosen, the Sorrows thought Daniel was talking about the same person.

You can try to tell Daniel that they are confused, but he will not understand what you mean (because it's really one of the least-intelligent sounding dialog choices the Courier can make) and basically get pissed off at you.