First,
Little Children cannot sin, but are Born in Sin?
We are Born in sin or a world of sin, and are influenced by the sins of others as soon as we are Born, and will probably reflect that later in life, but as children we cannot sin, because we don't have a full comprehension of what sin is.
Second,
Multiply & Subdue after or before the Tree of Knowledge
Even though God commanded them to multiply, they obviously didn't comply until after they partook of the "Fruit". Before that , they did not have a full understanding of what God wanted. Genesis shows that they followed that commandment after they partook of the fruit.
Thirdly,
Darkness 3 days or 3 hours?
Well these events are happening at different places, a part of America, and Israel. But it does say the "whole face of the earth". Well each is on a different side of the earth; it is round after all. But if it implies the whole atmosphere ( which they couldn't know or prove anyway) then there is a false translation in one of the texts, probably the Bibles, but that's if you didn't like my other explanation.
And finally (for now),
Perform Passover at Jerusalem only.
Well we are talking about two different groups of people, one who cannot travel to Jerusalem. And at that time Jerusalem was a wicked place, or destroyed. Even so, we don't have a fully detailed description of the Nephites religious practices except that they did observe the law atleast to the best of their abilities. They probably performed a passover like ceremony around their temples or greater cities.
I hope I helped.