Naked
The first reference to being naked in this text is this:
I am the one who received revelation from the fullness of imperishability,
who was summoned by the one who is great,
who obeyed the [master].
It is he who passed through the [worlds without being recognized],
who [came down after] stripping off his clothing,
and walked about naked,
who was found in perishability
though destined to be brought up to imperishability.
who was summoned by the one who is great,
who obeyed the [master].
It is he who passed through the [worlds without being recognized],
who [came down after] stripping off his clothing,
and walked about naked,
who was found in perishability
though destined to be brought up to imperishability.
Compare this to how Paul describes the afterlife or resurrection as being clothed (and not found naked) in 2 Corinthians 5:
1 Now we know that if the earthly tent we live in is dismantled, we have a building from God, an eternal house in heaven, not built by human hands. 2 For in this tent we groan, longing to be clothed with our heavenly dwelling, 3 because when we are clothed, we will not be found naked. 4 So while we are in this tent, we groan under our burdens, because we do not wish to be unclothed but clothed, so that our mortality may be swallowed up by life.
Without the references to clothing and nakedness, but along the same theme, Paul wrote about putting on "the imperishable" and immortality in 1 Corinthians 15:
For this perishable body must put on the imperishable, and this mortal body must put on immortality.
Thus, in this first reference, the text of the Second Apocalypse of James equates being "found in perishability" and having "walked about naked," referring to the "clothing" of imperishability. It tells of how the son of the Father "passed through the [worlds]," "stripping off his clothing" of imperishability. His destiny is to once again "be brought up to imperishability," which is to be clothed.
The second reference to being naked is this one:
“Therefore I say to you, you who judge have been judged. You did not spare,
but you have been spared. Be sober and [recognize him. For the one] you
[judged is actually not the one you] thought......
[58] you did not know.
He was [the one]
whom he who created heaven and earth and dwelled in it
[could] not [see].
He was the one [who] is life.
He was the light.
He was the one who will be
and will provide an ending for [what] has begun
and a beginning for what will come to an end.
He was the holy Spirit
and the invisible one
who did not come down on the earth.
He was the virgin,
and what he wishes happens to him.
I saw he was naked,
and there was no garment clothing him.
What he wills happens to him.......
but you have been spared. Be sober and [recognize him. For the one] you
[judged is actually not the one you] thought......
[58] you did not know.
He was [the one]
whom he who created heaven and earth and dwelled in it
[could] not [see].
He was the one [who] is life.
He was the light.
He was the one who will be
and will provide an ending for [what] has begun
and a beginning for what will come to an end.
He was the holy Spirit
and the invisible one
who did not come down on the earth.
He was the virgin,
and what he wishes happens to him.
I saw he was naked,
and there was no garment clothing him.
What he wills happens to him.......
This one also mentions some themes involving this one coming down to earth (through the statement "He was the holy spirit and the invisible one who did not come down to earth"), presented as a reference to a form where he had not come down to earth. The reference to "the virgin" may then be a reference to the virgin birth story, presented as a denial that he was born of a virgin, by saying that he actually was the virgin. When he had come down, it was possible to see that "he was naked, and there was no garment clothing him" because he is found in perishability, as discussed with reference to the previous passage.
Clothed
The first reference to clothing is the same one just mentioned:
I am the one who received revelation from the fullness of imperishability,
who was summoned by the one who is great,
who obeyed the [master].
It is he who passed through the [worlds without being recognized],
who [came down after] stripping off his clothing,
and walked about naked,
who was found in perishability
though destined to be brought up to imperishability.
who was summoned by the one who is great,
who obeyed the [master].
It is he who passed through the [worlds without being recognized],
who [came down after] stripping off his clothing,
and walked about naked,
who was found in perishability
though destined to be brought up to imperishability.
Where it reads as a reference to the clothing of imperishability.
The next reference to clothes is this one:
[Those who live] in forgetfulness [56]
are instructed in these things with [you].
Because of you
[they] will be taught about [these things]
and come to rest.
Because of you
they will come to reign
and become kings.
Because of [you]
pity will be taken
on those to be pitied.
As you are the first
who clothed yourself,
so also are you the first
who will strip off your clothes.
And you will become as you were
before you took off your clothes.’
are instructed in these things with [you].
Because of you
[they] will be taught about [these things]
and come to rest.
Because of you
they will come to reign
and become kings.
Because of [you]
pity will be taken
on those to be pitied.
As you are the first
who clothed yourself,
so also are you the first
who will strip off your clothes.
And you will become as you were
before you took off your clothes.’
The references regarding "come to rest" and "come to reign and become kings" are references to the enjoyment of salvation.
The reference to "become as you were before you took off your clothes" recalls the earlier statements about the son of the Father, who stripped off his clothing, was found naked in perishability, and then was brought up into the clothing of imperishability again.
Just before this, there is a reference to how we also existed before this world, being forced into it, thus being trapped in this place:
I know that everyone who [was] forced down to this place will come [to me like] little children.
The reference to being "the first who will strip off your clothes" is plausibly a reference to the efficacy of baptism, where one strips off their clothes to be baptized and thus to be saved. This allows him to "become as you were before you took off your clothes," i.e. to become as you were before entering the world and being trapped in that place.
The next reference to clothing has already been mentioned:
He was the Holy Spirit and the Invisible One, who did not descend upon the earth. He was the virgin, and that which he wishes, happens to him. I saw that he was naked, and there was no garment clothing him. That which he wills, happens to him [...].
Which has already been discussed, as a reference to the son of the Father being found in perishability and thus naked.
Ambiguity
It should be mentioned that ambiguity is a seemingly intentional feature of this language. It enhances the revelatory character of the dialogue to provide the statements indirectly, which can be a kind of genre feature. So it is necessary to provide interpretation if there is any chance of recovering what the author is trying to say.
The only thing we can do is to attempt to pay careful attention to context and hope to see indications of what readings are a best fit.
I hope that this discussion has helped to clarify one aspect of the Second Apocalypse of James.