You had some problems with Lehi and Nephi's visions of the Tree of Life. If you would like to truly understand what they are talking about, you ought to try and draw a picture of the vision. I have a friend who did just that and for the first time was able to really picture what was happening. There is the Tree of Life in the vision, which is the love of God, and an iron rod leading to it which iron rod is the scriptures. There are mists of darkness which engulf the path that iron rod leads along, representing the temptations of the world, meaning that if one doesn't cling to the scriptures and hold fast to them, they will get lost and fall off of the path leading to God (repentance can bring them back, along with scripture study). Alongside the path, there is a river. If you had quoted the next verse, it would be clear that they are not the same thing. God, or more specifically His love, or living water as Christ called himself, is represented by the tree of life, which all the righteous are striving to attain. 1 Nephi 8:13 "I beheld a river of water; and it ran along and it was near the tree of which I was partaking the fruit" The tree (living waters) and the river are definitely separate, the one representing that which is most desirable, and the other that which is the least desirable. 1 Nephi 15:26-29 "And they said unto me: what meaneth the river of water which our father saw? And I said unto them that the river of water was filthiness; and so much was his mind swallowed up in other things that he beheld not the filthiness of the water. And I said unto them that it was an awful gulf, *which separated the wicked from the tree of life*, and also from the saints of God. And I said unto them that it was a representation of that awful hell, which the angel said unto me was prepared for the wicked." Is that easier to understand?
You are referring to the article, "How to Use the Book of Mormon." Though I am not the author, I'll attempt to answer the point.
In 1 Nephi 8, Lehi has a vision which is recorded in detail. "And as I cast my eyes round about, that perhaps I might discover my family also, I beheld a river of water; and it ran along, and it was near the tree of which I was partaking the fruit. And I looked to behold from whence it came; and I saw the head thereof a little way off; and at the head thereof I beheld your mother, Sariah and Sam, and Nephi; and they stood as if they knew not whither they should go. ... And it came to pass that I was desirous that Laman and Lemuel should come and partake of the fruit also; wherefore , I cast mine eyes towards the head of the river, that perhaps I might see them. And it came to pass that I saw them, but they would not come unto me and partake of the fruit." (verses 13-14, 16-17).
The vision is explained in chapter 11 by Lehi's son, Nephi. "And the angel said unto me: Behold the Lamb of God, yea, even the Son of the Eternal Father! Knowest thou the meaning of the tree which thy father saw? And I answered him, saying: Yea, it is the love of God, which sheddeth itself abroad in the hearts of the children of men; wherefore, it is the most desirable above all things. ... And it came to pass that I beheld that the rod of iron, which my father had seen, was the word of God, which led to the fountain of living waters, or to the tree of life; which waters are a representation of the love of God; and I also beheld that the tree of life was a representation of the love of God." (verses 21-22, 25)
In chapter 12, Nephi has a vision that returns to his father's vision, but the interpretation has changed. "And the angel spake unto me, saying: Behold the fountain of filthy water which thy father saw; yea, even the river of which he spake; and the depths thereof are the depths of hell." (verse 16)
In chapter 15, the topic comes up again. "And they said unto me: What meaneth the river of water which our father saw? And I said unto them that the water which my father saw was filthiness; and so much was his mind swallowed up in other things that he beheld not the filthiness of the water." (verses 26-27).
So the vision is of a tree with a river flowing by it, whose headwaters is a fountain nearby. In the first explanation, both the tree and the river are said to represent the love of God. But later, in explaining why the people couldn't cross, we are told that the water was filthy and represents the depths of hell. When asked later why Nephi didn't mention the water being filthy, well, that was because he was too caught up in the vision to notice.
But the point remains. At one point the water is referred to as the love of God and at another, it is the filthy depths of hell. Your explanation that the tree of life and the living waters in chapter 11 are the same thing does not match what is said. I know you desire it to be consistent, to the point that you are willing to bend the words of your own book, but it remains that it isn't what was said.