"Therefore we are always confident and know that as long as we are at home in the body we are away from the Lord. For we live by faith, not by sight. We are confident, I say, and would prefer to be away from the body and at home with the Lord." - 2 Cor.5:6
"If I am to go on living in the body, this will mean fruitful labor for me. Yet what shall I choose? I do not know! I am torn between the two: I desire to depart and be with Christ, which is better by far; but it is more necessary for you that I remain in the body. - Phil.1:22-24
It is always important to compare and cross-reference other scriptures to arrive at a right conclusion. As you can see from the scriptures above, to be absent from the body is to be in the presence of the Lord. These are stating that at the time of death the spirit departs from the body and goes to be in the presence of the Lord. Therefore, in John 3:13 Jesus must be saying something other than what you think it is saying. In order to understand what the Lord means, we must look at the whole context, which I've included below:
"No one has ascended into heaven except the One who descended from heaven—the Son of Man. Just as Moses lifted up the snake in the wilderness, so the Son of Man must be lifted up, that everyone who believes in Him may have eternal life."
Therefore, Jesus is saying that no other man has come down from heaven (which is true)and will have resurrected and gone back up into heaven, which is what Jesus is referring to when he tells Nichodemus regarding his being lifted up like the bronze serpent, i.e. his being crucified. Therefore, Christ came down from heaven, was crucified, resurrected and went back up into heaven, which is what no other man has done. This does not interfere with the other scriptures listed above, which reveal that the at the time of death a believers [spirit] departs and goes to be in the presence of the Lord. It is not until the resurrection that men will follow Christ in their resurrected bodies, but they did not start from heaven has He did.
"Suddenly two men, Moses and Elijah, began talking with Jesus. They appeared in glory and spoke about His departure, which He was about to accomplish at Jerusalem."
But we must use the event of Moses and Elijah appearing with Jesus because you don't have a conversation with a vision, which is what Moses and Elijah were doing in the scripture above. In your reference to them being a vision, you are inferring that they were like inanimate projections, yet the scripture tells us that they were having a conversation with Jesus about his departure. Also, there is a scripture that states that "the women saw a vision of angels" translated from "optasia" which means to see a supernatural appearance.
Once again, you need to cross-reference and compare scripture. First of all regarding us being "spirits" after resurrection and appearing to his disciples, Jesus said the following:
"While they were describing these events, Jesus Himself stood among them and said, “Peace be with you.” But they were startled and frightened, thinking they had seen a spirit.
“Why are you troubled,” Jesus asked, “and why do doubts arise in your hearts? Look at My hands and My feet. It is I Myself. Touch Me and see—for a spirit does not have flesh and bones, as you see I have.”
So, in the scripture above, Jesus appears to his disciples who are frightened because they think he is a spirit. But Jesus comforts them and reassures them that it is he himself, which he proves by showing them the nail marks in his hands and feet. As further proof that Jesus was in his resurrected body he tells them, "a spirit does not have flesh and bones, as you see I have."
Jesus resurrected in the same body that he was crucified in, albeit glorified and immortal. The same body that he appeared to the disciples in, the same body that he ascended in and sits at the right hand of the Father in. And is the same body that he will return in when he appears to gather the church, where at which when we see him, we shall be like him, being transformed into those immortal and glorified bodies just like his resurrected body of flesh and bones, but with heavenly abilities.
I hope that you will consider these scriptures and understand that, when a believer dies their spirit departs and goes immediately to be in the presence of the Lord. And that when the resurrection takes place, the spirits of those who have died in Christ he will bring with him where they will be reunited with their resurrected bodies of flesh and bone like Christ's, but immortal and glorified.