I hope that as you read these things you'll be aware of how you feel, that you will be able to feel the love our Heavenly Father has for you, and that the things I'm saying are true. I, myself, know and believe them to be true.
So in accordance with the reference in D&C 130:3 & how it contradicts the verse in Alma, let me explain. In D&C 130:3 it is talking about how the fact that "The Father and the Son dwell in a man's heart is an old sectarian notion, and is false." You have to read the full context (the whole section) in order to understand this verse. This whole section is about the Father and the Son. It is true, the Father and Son can't literally dwell within us because as you'll read in the same section in verse 22 "The Father has a body of flesh and bones as tangible as man's; and the Son also..." So think about it, how can a man with flesh & bones dwell within a person that is also flesh & bones like us? You can't, which makes vs: 3 true. However, his spirit can abide with us. Its like saying that those that have died, their spirits are still with us. I'm not saying the Father and the Son are dead ... just I'm trying to make a connection with how it might feel like.
And in connection with that. in Alma 34:36 when it says says, “And this I know, because the Lord hath said he dwelleth not in unholy temples, but in the hearts of the righteous doth he dwell.” This is referring to our bodies, just like it says in I Corinthians 3:16-17 "Know ye not that ye are the temple of God, and that the Spirit of God dwelleth in you? If any man defile the temple of God, him shall God destroy; for the temple of God is holy, which temple ye are." So, the Lord's spirit cannot dwell in people that live unrighteously. Does that make sense? His actual body doesn't dwell in us, but if we remain righteous then His spirit can abide within us.
Then you talked about D&C 84:4-5 and about the prophesies of the Civil War and the Independance, Missouri temple. I know that he was talking about the wars in general, in verse 2, and saying how in the last days wars will be poured out on all nations. Clearly you can see this coming to pass with the war in Uganda, Iraq and many other places. Then in verse 3 it describes the civil war. Then in D&C 84:4-5 when it talks about the temple being built in Independence, Missouri during "this generation." There is no such temple yet, you're true, due to the fact that the Community of Christ Church owns the lot that the temple will be built on. But we know that in the last days a temple will be built there. I do not doubt that. And the temple lot is there. So no worries there, it will happen.
I'm glad to see that you are actually attempting to look at the accuracy of Mormon teaching since very few wish to handle the difficulties Mormonism presents to the intellect. For myself, I am a believer of Jesus Christ and follow His book, which is commonly called the Holy Bible. Since you are willing to use that book as evidence, I will freely make use of it in my reply.
Since everyone doesn't have access to the Doctrines and Covenants, let's start by quoting the larger context, since you charge that the context wasn't considered:
"When the Savior shall appear we shall see him as he is. We shall see that he is a man like ourselves. And that same sociality which exists among us here will exist among us there, only it will be coupled with eternal glory, which glory we do not now enjoy. John 14:23 — The appearing of the Father and the Son, in that verse, is a personal appearance; and the idea that the Father and the Son dwell in a man’s heart is an old sectarian notion, and is false. ... The Father has a body of flesh and bones as tangible as man’s; the Son also; but the Holy Ghost has not a body of flesh and bones, but is a personage of Spirit. Were it not so, the Holy Ghost could not dwell in us." (Doctrine and Covenants, 130:1-3, 22).
"And this I know, because the Lord hath said he dwelleth not in unholy temples, but in the hearts of the righteous doth he dwell; yea, and he has also said that the righteous shall sit down in his kingdom, to go no more out; but their garments should be made white through the blood of the Lamb." (Book of Mormon, Alma 34:36).
Your point is that Joseph Smith was arguing from a physical standpoint while in the book of Alma he was talking from a spiritual standpoint. What you are overlooking is that Joseph Smith was commenting on John 14:23 and saying that what appears in John 14:23 was "an old sectarian notion, and is false."
"Jesus answered and said to him, "If anyone loves Me, he will keep My word; and My Father will love him, and We will come to him and make Our home with him" (John 14:23).
I'm curious how you come to the conclusion that I Corinthians 3:16-17 is speaking in a spiritual sense, but you don't apply the same logic to John 14:23. And if you can understand this, then why would Joseph Smith declare this verse to be false?
The actual problem is that Joseph Smith held the idea that God is a physical being, something that is not taught in the Book of Mormon because it appears Joseph Smith developed the idea at a later point in his life. (Doctrine and Covenant 130 was written in 1843, about 13 years after the Book of Mormon was published.) In that same chapter of Alma, the Book of Mormon states: "And then Ammon said: Believest thou that there is a Great Spirit? And he said, Yea. And Ammon said: This is God. And Ammon said unto him again: Believest thou that this Great Spirit, who is God, created all things which are in heaven and in the earth?" (The Book of Mormon, Alma 18:26-28).
The concept that God is a physical being is contradictory to what God has always taught about Himself. "God is Spirit, and those who worship Him must worship in spirit and truth" (John 4:24). Even the Old Testament understood this. In discussing the superiority of God, Isaiah points out, "Now the Egyptians are men, and not God; and their horses are flesh, and not spirit. When the LORD stretches out His hand, both he who helps will fall, and he who is helped will fall down; they all will perish together" (Isaiah 31:3). Thus Joseph Smith's later position contradicted both himself and the teachings of the Bible.
"Yea, the word of the Lord concerning his church, established in the last days for the restoration of his people, as he has spoken by the mouth of his prophets, and for the gathering of his saints to stand upon Mount Zion, which shall be the city of New Jerusalem. Which city shall be built, beginning at the temple lot, which is appointed by the finger of the Lord, in the western boundaries of the State of Missouri, and dedicated by the hand of Joseph Smith, Jun., and others with whom the Lord was well pleased. Verily this is the word of the Lord, that the city New Jerusalem shall be built by the gathering of the saints, beginning at this place, even the place of the temple, which temple shall be reared in this generation. For verily this generation shall not all pass away until an house shall be built unto the Lord, and a cloud shall rest upon it, which cloud shall be even the glory of the Lord, which shall fill the house." (Doctrine and Covenants 84:2-5).
Now we have a bit of a problem here. You state that the timeframe is a war involving all nations, yet there is no mention of war in this quote. Nor does verse three mention the civil war. You might have been told that other time frames are involved, but clearly this is not what Joseph Smith wrote or meant. What is even more interesting is that following these verses are instructions for the organization of the Mormon church. Now if you expect people to accept that this is talking about something in the future, then it would follow that the Mormon church remains in the future as well.
But what we see is that verse two speaks of a gathering of saints and verse four speaks that the gathering saints would build a temple in this generation. Thus verses two through five are tied to the same timeframe. In addition, Joseph Smith said "this generation," thus addressing the people receiving his prophecy. If it was meant for another people, he would have said "that generation." Again, a bit later Smith said, "Therefore, as I said concerning the sons of Moses—for the sons of Moses and also the sons of Aaron shall offer an acceptable offering and sacrifice in the house of the Lord, which house shall be built unto the Lord in this generation, upon the consecrated spot as I have appointed— And the sons of Moses and of Aaron shall be filled with the glory of the Lord, upon Mount Zion in the Lord’s house, whose sons are ye; and also many whom I have called and sent forth to build up my church." (Doctrine and Covenants, 84:31-32). Once again, if "this generation" is in the future, then the Mormon church has yet to be established because it was to be done by "this generation."
Earlier Mormons tried to salvage this prophecy by claiming that a generation was longer than you might expect. Thus they put a footnote in their late 1800's edition of the Book of Mormon on the word generation in this passage which said, "a generation does not all pass away in one hundred years." But 1932 has come and gone with no temple being built and the footnote was removed from the Book of Mormon. George Q. Cannon wrote, "A temple shall be reared in the Center Stake of Zion in the generation in which the revelation was given." (Journal of Discourses, vol. 10, p. 344, October 23, 1864); thus defining which generation very clearly. Joseph Fielding Smith understood that the prophecy was intended to talk about the generation in 1832:
"It may be reasonable to assume that in giving this revelation to the Prophet the Lord did have in mind the generation of people who would still be living within the one hundred years from the time of the announcement of the revelation, and that they would enjoy the blessings of the temple, and a glorious cloud would rest upon it. It is also reasonable to believe that no soul living in 1832, is still living in mortality on the earth.” (Answers to Gospel Questions, 4:112).
Joseph Fielding Smith's answer to this dilemma was to claim that God changed His mind and no longer expects people to uphold this prophecy. So why do you espouse a view different from your past leaders?
A simple search, however, of the Doctrine and Covenants shows that Smith used "this generation" to refer to those he was addressing, not some vague future group. He had fully expected in 1832 to have a temple built in Missouri in a few years. In fact, he said, "the churches should "be in readiness to move to Jackson county in two years from the eleventh of September next, which is the appointed time for the redemption of Zion. ... you will learn by this we have a great work to do, and but little time to do it in;" (History of the Church, vol. 2, p. 145, August 16, 1834). Of course, it never came about, thus proving Smith to be a false prophet.
"But the prophet who presumes to speak a word in My name, which I have not commanded him to speak, or who speaks in the name of other gods, that prophet shall die. And if you say in your heart, 'How shall we know the word which the LORD has not spoken?' -when a prophet speaks in the name of the LORD, if the thing does not happen or come to pass, that is the thing which the LORD has not spoken; the prophet has spoken it presumptuously; you shall not be afraid of him" (Deuteronomy 18:20-22).