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I am not sure if what Peter, James and John saw is valid as it speaks about his “departure,” which would predates his return.

I think it is obvious what Jesus meant since the incident on the Mount of Transfiguration happened a little over a week after Jesus said it.

In Mark 14:61-62, Jesus declares that the high priest who delivered him over to the Romans for execution will see the Son of Man coming on the clouds of heaven.

Again the high priest questioned Him, “Are You the Christ, the Son of the Blessed One?” “I am,” said Jesus, “and you will see the Son of Man sitting at the right hand of Power and coming with the clouds of heaven.”

But He didn't say they would see this shortly, just that they WOULD see Him one day. And we know that one day at the name of Jesus every knee should bow, in heaven and on earth and under the earth, and every tongue confess that Jesus Christ is Lord, to the glory of God the Father. (Philippians 2:10,11). We also are told:

The Return of the Son of Man

Immediately after the tribulation of those days: ‘The sun will be darkened, and the moon will not give its light; the stars will fall from the sky, and the powers of the heavens will be shaken.’ At that time the sign of the Son of Man will appear in heaven, and all the tribes of the earth will mourn. They will see the Son of Man coming on the clouds of heaven, with power and great glory. And He will send out His angels with a loud trumpet call, and they will gather His elect from the four winds, from one end of the heavens to the other. (Matt. 24:29-31).

Then in John 21:22-23, Jesus says that the Apostle John will remain alive until His return.

Actually, no, Jesus didn't say that. What He said was:

Peter turned and saw the disciple whom Jesus loved following them. He was the one who had leaned back against Jesus at the supper to ask, “Lord, who is going to betray You?” When Peter saw him, he asked, “Lord, what about him?” Jesus answered, “If I want him to remain until I return, what is that to you? You follow Me!” Because of this, the rumor spread among the brothers that this disciple would not die. However, Jesus did not say that he would not die, but only, “If I want him to remain until I return, what is that to you?”

As for your other points, we ought to believe what God tells us and not try to second guess or accuse Him of contradicting Himself. We can trust in the authority of God's word because it IS His word and "heaven and earth will pass away, but the word of our God will never pass away". If He says he will create a new heavens and new earth where righteousness dwells and which will no longer have any taint of sin, then I believe Him. The Apostle Peter writes that:

But the Day of the Lord will come like a thief. The heavens will disappear with a roar, the elements will be destroyed by fire, and the earth and its works will be laid bare. Since everything will be dissolved in this way, what kind of people ought you to be? You ought to conduct yourselves in holiness and godliness as you anticipate and hasten the coming of the day of God, when the heavens will be destroyed by fire and the elements will melt in the heat. (II Peter 3:10-12)

This is a rather long response; but, I truly hope that you do read it. TO quote you:
As for your other points, we ought to believe what God tells us and not try to second guess or accuse Him of contradicting Himself. We can trust in the authority of God's word because it IS His word and "heaven and earth will pass away, but the word of our God will never pass away". If He says he will create a new heavens and new earth where righteousness dwells and which will no longer have any taint of sin, then I believe Him

This is well and good, in fact no sounder advice can be given; however, whose words and whose understanding is deciding "what" was said?

Quoting you further:

The Return of the Son of Man
Immediately after the tribulation of those days: ‘The sun will be darkened, and the moon will not give its light; the stars will fall from the sky, and the powers of the heavens will be shaken.’ At that time the sign of the Son of Man will appear in heaven, and all the tribes of the earth will mourn. They will see the Son of Man coming on the clouds of heaven, with power and great glory. And He will send out His angels with a loud trumpet call, and they will gather His elect from the four winds, from one end of the heavens to the other. (Matt. 24:29-31).

Specifically, ‘The sun will be darkened, and the moon will not give its light; the stars will fall from the sky, and the powers of the heavens will be shaken.’

Please, do not just give face value to the above Scripture; there is SO VERY much more stated in that one sentence than I believe you have ever imagined'

Please read on......
There are not very many people who remember what happened in the old testament when Israel would backslide and start worshiping other Gods. God would send a prophet who would tell them that a day of the Lord was coming, which always symbolized judgment. There would be a lot of talk about it being a cloudy day or a lot of talk about the sun moon and stars falling or getting dark.

Judgment against Egypt
Ezekiel 32:7-8 And when I shall put thee out I will cover the heaven and make the stars thereof dark; I will cover the sun with a cloud, and the moon shall not give her light. All the bright lights of heaven will I make dark over thee.

This is another good example of how the constellation an (heavens, sun and stars) were not literally darkening, but God was using another nation to judge Babylon.
Judgment on Babylon

Isaiah 13:9-11 See, the day of the LORD is coming a cruel day, with wrath and fierce anger to make the land desolate and destroy the sinners within it. 10 The stars of heaven and their constellations will not show their light. The rising sun will be darkened and the moon will not give its light. 11 I will punish the world for its evil, the wicked for their sins. I will put an end to the arrogance of the haughty and will humble the pride of the ruthless.

Here are some other examples-

Joel 2:10 The earth shall quake before them; the heavens shall trimble. The sun,moon shall be dark, and the stars shall withdrawal their shining.

Amos 8:9 And it shall come to pass in that day saith the Lord God, that I will cause the sun to go down at noon, and I will darken the earth in a clear day

The big question is, when did heaven and earth pass, or has it passed at all. Hebrews 12 gives some excellent insight concerning this issue:

Hebrews 12:18-27 18You have not come to a mountain that can be touched and that is burning with fire; to darkness, gloom and storm; 19to a trumpet blast or to such a voice speaking words that those who heard it begged that no further word be spoken to them, 20because they could not bear what was commanded: "If even an animal touches the mountain, it must be stoned to death." 21The sight was so terrifying that Moses said, "I am trembling with fear." 22But you have come to Mount Zion, to the city of the living God, the heavenly Jerusalem. You have come to thousands upon thousands of angels in joyful assembly, 23to the church of the firstborn, whose names are written in heaven. You have come to God, the Judge of all, to the spirits of the righteous made perfect, 24to Jesus the mediator of a new covenant, and to the sprinkled blood that speaks a better word than the blood of Abel. 25See to it that you do not refuse him who speaks. If they did not escape when they refused him who warned them on earth, how much less will we, if we turn away from him who warns us from heaven? 26At that time his voice shook the earth, but now he has promised, "Once more I will shake not only the earth but also the heavens." 27The words "once more" indicate the removing of what can be shaken-that is, created things-so that what cannot be shaken may remain.
Notice the words heaven and earth. Also notice the use of the present tense to describe what was taking place at this time:
"... And this word, Yet once more, signifieth the removing of those things that are being shaken (Old Covenant), as of things that are made, that those things which cannot be shaken (New Covenant) may remain."

We see that the Old Covenant that was decaying (present tense) and waxing old (present tense) was ready to vanish away. With the destruction of their Temple (the centerpiece of the Jewish Old Covenant system), the Old Covenant had completely waxed old and vanished away. The Heaven and Earth had passed away. This would explain Isaiah 51, a passage that compares the temporal quality of the law versus the eternal quality of the New Covenant salvation: Isaiah 51:6 Lift up your eyes to the heavens, and look upon the earth beneath: for the heavens shall vanish away like smoke, and the earth shall wax old like a garment, and they that dwell therein shall die in like manner: but my salvation shall be for ever, and my righteousness shall not be abolished.

Again, compare with:
Hebrews 8:13 By calling this covenant "new," he has made the first one obsolete; and what is obsolete and outdated will soon disappear.

Even Psalms speaks of this:
Psalms 102:25-26 Of old hast thou laid the foundation of the earth: and the heavens are the work of thy hands. {26} They shall perish, but thou shalt endure: yea, all of them shall wax old like a garment; as a vesture shalt thou change them, and they shall be changed: Some may ask whether this affects Revelation 21: Revelation 21:1 And I saw a new heaven and a new earth: for the first heaven and the first earth were passed away; and there was no more sea.

As far as Revelation 21 is concerned, the question may be raised: What about the fact that the passage says there was no more sea? First, I think we should realize how the Bible uses sea. Of course John drew many of his metaphors and apocalyptic language from the rest of the Bible. It would seem inconsistent to suddenly literalize the first verse of Revelation 21. Consider these uses of sea and those to whom it refers:

Isaiah 60:1-5 Arise, shine; for thy light is come, and the glory of the LORD is risen upon thee. {2} For, behold, the darkness shall cover the earth, and gross darkness the people: but the LORD shall arise upon thee, and his glory shall be seen upon thee. {3} And the Gentiles shall come to thy light, and kings to the brightness of thy rising. {4} Lift up thine eyes round about, and see: all they gather themselves together, they come to thee: thy sons shall come from far, and thy daughters shall be nursed at thy side. {5} Then thou shalt see, and flow together, and thine heart shall fear, and be enlarged; because the abundance of the sea shall be converted unto thee, the forces of the Gentiles shall come unto thee.

Sea here is obviously referring to the Gentiles. This passage speaks of a uniting of Gentiles and Israelites. This is remarkably similar to Ephesians 2:

Ephesians 2:11-19 Wherefore remember, that ye being in time past Gentiles in the flesh, who are called Uncircumcision by that which is called the Circumcision in the flesh made by hands; {12} That at that time ye were without Christ, being aliens from the commonwealth of Israel, and strangers from the covenants of promise, having no hope, and without God in the world: {13} But now in Christ Jesus ye who sometimes were far off are made nigh by the blood of Christ. {14} For he is our peace, who hath made both one, and hath broken down the middle wall of partition between us; {15} Having abolished in his flesh the enmity, even the law of commandments contained in ordinances; for to make in himself of twain one new man, so making peace; {16} And that he might reconcile both unto God in one body by the cross, having slain the enmity thereby: {17} And came and preached peace to you which were afar off, and to them that were nigh. {18} For through him we both have access by one Spirit unto the Father. {19} Now therefore ye are no more strangers and foreigners, but fellowcitizens with the saints, and of the household of God;
The Psalmist speaks of the prophecy that God would gather the Israelites that were scattered among the nations or the sea:

Psalms 68:22 The Lord said, I will bring again from Bashan, I will bring my people again from the depths of the sea: The Psalmist also makes a distinction between the sea versus those upon the earth:

Psalms 65:5 By terrible things in righteousness wilt thou answer us, O God of our salvation; who art the confidence of all the ends of the earth, and of them that are afar off upon the sea:

It is interesting here how the Psalmist describes those upon the sea as "afar off." That is how Paul describes the Gentiles in Ephesians 2:

Ephesians 2:13 But now in Christ Jesus ye who sometimes were far off are made nigh by the blood of Christ.

There would be no more strangers or Gentiles in this land.

There would be no more sea. It would be a New Heaven and a New Earth wherein would dwell righteousness. The union would be those in Christ Jesus.

I believe this is a consistent explanation of the significance of the terms heaven and earth and sea and their relationship with the Messianic kingdom.

I apologize for such a brief study on this; there are dozens and dozens of examples. There is always two sides to anything spoken:
1. What is said.
2. What is understood.

Let us allow Scripture be our interpreter. Final words.....

Sir Isaac Newton (1642-1727)
"The figurative language of the prophets is taken from the analogy between the world natural and an empire or kingdom considered as a world politic. Accordingly, the world natural, consisting of heaven and earth, signifies the whole world politic, consisting of thrones and people, or so much of it as is considered in prophecy; and the things in that world signify the analogous things in this. For the heavens and the things therein signify thrones and dignities, and those who enjoy them: and the earth, with the things thereon, the inferior people; and the lowest parts of the earth, called Hades or Hell, the lowest or most miserable part of them. Great earthquakes, and the shaking of heaven and earth, are put for the shaking of kingdoms, so as to distract and overthrow them; the creating of a new heaven and earth, and the passing of an old one; or the beginning and end of a world, for the rise and ruin of a body politic signified thereby. The sun, for the whole species and race of kings, in the kingdoms of the world politic; the moon, for the body of common people considered as the king's wife; the starts, for subordinate princes and great men; or for bishops and rulers of the people of God, when the sun is Christ. Setting of the sun, moon, and stars; darkening the sun, turning the moon into blood, and falling of the stars, for the ceasing of a kingdom." (Observations on the Prophecies, Part i. chap. ii)