"(Sounds a lot like the Flying Spaghetti Monster too, btw)."
Do you have a book by the Flying Spaghetti Monster written millennia before this evidence was discovered or are you inventing him post hoc?
"1) Everything that begins to exist has a cause (in this case time, space and matter). Who says? When we get down to the quantum level, this cause & effect business seems to cease to have the same meaning and predictability that it does above it. So, it may well not be true in physics that everything that begins to exist must have a cause. And if not everything has to, why does the universe?"
To deny the law of cause and effect shows just how desperate atheists can get to avoid the logical conclusion that God exists. At the quantum level, predictability gets touchy but just because we can't predict a cause doesn't mean there isn't one. Cause and effect is the foundation of science. I tell ya . . . if atheists had started science it would have never got off the ground.
"When do we decide when something "began to exist" since absolutely everything we see around us is merely a reconfiguration of existing matter?"
You began to exist the moment your father's sperm joined with your mother's ovum. You did not exist before that. The material your are composed of existed but it was not you. Oh, the tap dancing that must be done. If I made irrational arguments like this, I'd never hear the end of it. I'm imploring people to look at the facts we can actually observe while atheist must resort to denying fundamental laws of physics and logic.
"3) Why must the cause be immaterial, non-spatial and timeless? What can you possibly know about any event or thing that happened before the universe even existed that could lead you to state it "must" be anything?"
The cause of matter must be immaterial. Otherwise, matter would already have to exist to cause itself. Irrational. Same goes for time and space. It is not an argument that will persuade everyone. But then, NO argument will persuade EVERYONE. Even an argument as water-tight as the Kalam Cosmological Argument.
"4) How do you know that any "cause" must be a sentient intelligence?"
The Kalam argument can't get you there - and it's not meant to. The Moral Argument gets you to a personal God. It's a cumulative case.
"5) What would lead you to conclude (if the above turned out to be true) that the sentient intelligence chose to incarnate himself as a mortal on our planet in order to have him sacrificed to himself?"
Because He said He did and everything else He said has come true so I trust Him on faith - but not blind faith. I'm sure if I felt like it I could turn everyone of those questions around and demolish naturalism too.
It ultimately always comes down to which view is more reasonable to believe. We determine that by who has more supporting evidence and is logically consistent. Atheism fails on both grounds. I would actually prefer to be an atheist. But I care more about truth than what feels good or is comforting.