Q: If you do everything, you do "it all". If you do something anew from the very start, you do it "all over again".
Now - if you do everything anew from the very start, and you want to emphasize that you really do every bit of it, do you do "it all all over again" or "it all over again"? Or are both equivalent?
A1: I would say I'll "do everything over again." I don't like a doubled "all," even if you put a comma between them. I suppose "do everything all over again" would work for serious emphasis.
A2: If you want to emphasize that you redo the whole thing, you do indeed "do it all all over again". At least, I would.