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As for "God" and "The Lord" this is plain as day. Gen 1.1 uses the word GOD, while gen 2 starts the usage of the word "The Lord". "God" implies Judgement, while "The Lord" implies Mercy. There are many names for God, each with different implications. What this means is that 'God' created the heavens and the earth using Judgement (He saw that it was Good). Later, when he created man, he balanced this judgement with Mercy. He perceived that the world could survive on Justice alone (Rashi).

The phrase "not yet" appears several times in the bible. Gen 2.5 "And every shrub of the field was not yet in the earth and every shrub...had not yet sprung up" shows that they had been created, but were not yet above the surface of the ground... like germinating seeds.

Sorry, meant to say the world could NOT survive on Justice alone.

It is a common mistake to think that the order listed is the order of Creation. This is not true, because "In the beginning God Created the heavens and the earth" and "The spirit of God hovered over the waters" implies, obviously, that the waters were already being created.

The phrase "in the beginning" is used often in scripture... it does not mean "At first". It means in the beginning of creating -- not necessarily chronological. You need the context of the remaining text to figure out the order.