In his book "TRUTH IN TRANSLATION: Accuracy and Bias in English Translations of the New Testament", Jason David BeDuhn, an associate professor of religious studies at Northern Arizona University, analizes ten major English translations (including KJV) of the Greek scriptures and writes that the only two correct renderings are by the NRSV and the NWT. He states, "There is no reason to think that the 'Holy Spirit' is involved in this passage. Was Christ justified in or by the Holy Spirit? The parallel that is drawn is 'in flesh' rules out such a reading".

In his book "TRUTH IN TRANSLATION: Accuracy and Bias in English Translations of the New Testament", Jason David BeDuhn, an associate professor of religious studies at Northern Arizona University, analyzes ten major English translations (including KJV) of the Greek scriptures and writes that the only two correct renderings are by the NRSV and the NWT. He states, "There is no reason to think that the 'Holy Spirit' is involved in this passage. Was Christ justified in or by the Holy Spirit? The parallel that is drawn is 'in flesh' rules out such a reading".

In his book " TRUTH IN TRANSLATION Accuracy and Bias in English Translations of the New Testament" Jason David BeDuhn an associate professor of religious studies at Northern Arizona University, Analizes ten major English translations (including KJV) of the Greek scriptures , and writes that the only two correct renderings are by, NRSV and NW , and states "There is no reason to think that the" Holy Spirit" is involved in this passage. Was Christ justified in or by the Holy Spirit? The parallel that is drawn is "in flesh" rules out such a reading "

NRSV " He was revealed in flesh, vindicated[b] in spirit,[c] seen by angels,proclaimed among Gentiles, believed in throughout the world taken up in glory."

NW ( New World Translation) "He was made manifest in flesh, was declared righteous in spirit, appeared to angels, was preached about among nations, was believed upon in the world, was received up in glory."

The word "Θεοs" does not appear in either WHNU or the Nestle Aland critical edition of the Greek Testament on which most English translations are based. Noted below.  (NA) καὶ ὁμολογουμένως μέγα ἐστὶν τὸ τῆς εὐσεβείας μυστήριον· ὃς ἐφανερώθη ἐν σαρκί,ἐδικαιώθη ἐν πνεύματι, ὤφθη ἀγγέλοις, ἐκηρύχθη ἐν ἔθνεσιν, ἐπιστεύθη ἐν κόσμῳ, ἀνελήμφθη ἐν δόξῃ. (WHNU) και ομολογουμενως μεγα εστιν το της ευσεβειας μυστηριον ος εφανερωθη εν σαρκι εδικαιωθη εν πνευματι ωφθη αγγελοις εκηρυχθη εν εθνεσιν επιστευθη εν κοσμω ανελημφθη εν δοξη There are many different translations and no two are alike, I have noticed it and so have you, and your alarmed. The KJV was based on The Textus Receptus by Erasmus and not based on the ancient Greek Manuscripts . At the time the KJV was written,knowledge of the Greek Koine was very limited, further older manuscripts have been found which made it necessary to revise the bibles. Bias and beliefs of the translators also is a reason for the differences.

BELOW IS AN EXPLANATION OF THE VERSE 1 TIMOTHY 3:16 BASED ON SCRIPTURES. So what does it mean " vindicated in spirit" and " manifest in the flesh"mean? And what are the benefits to mankind?.

*MANIFEST IN THE FLESH Jesus, who was “the Word” of God, “out of heaven,” divested himself of spirit nature and “became flesh.” ( 1Cor. 15:47; Phil. 2:5-8; John 1:14;  ) That in being born as a human he was no spirit and that he did not merely assume a fleshly body, as angels had done in the past (Ge 18:1-3; 19:1; Jos 5:13-15), is attested to by the apostle John, who says that one is antichrist who denies that Jesus Christ came “in the flesh.” (1John 4:2, 3) In order to provide the ransom for mankind and thereby to help those who would be his associates in the heavenly calling, the Word became flesh, being born all human, no incarnation. The Bible tells us this: “Since the ‘young children’ are sharers of blood and flesh, he also similarly partook of the same things.” (Heb. 2:14-16) His earthly sojourn was spoken of as “the days of his flesh.” (Heb 5:7) “The bread that I shall give is my flesh in behalf of the life of the world,” Jesus said. He went on to state that those hoping to remain in union with him must ‘eat his flesh and drink his blood.’ Not appreciating the spiritual, symbolic significance of his words, some construed the statement as cannibalistic and were shocked.—Joh 6:50-60.

VINDICATED IN SPIRIT God’s Son. God’s “only-begotten son,” the Word, was a spirit person like his Father, hence “existing in God’s form” (Php 2:5-8), but later “became flesh,” residing among mankind as the man Jesus. (John 1, 14) Completing his earthly course, he was “put to death in the flesh, but [was] made alive in the spirit.” ( 1 Tim 3:16, 1Pe 3:18) His Father resurrected him, granted his Son’s request to be glorified alongside the Father with the glory he had had in his prehuman state (Joh 17:4, 5), and God made him “a life-giving spirit.” (1Co 15:45) The Son thus became again invisible to human sight, dwelling “in unapproachable light, whom not one of men has seen or can see.”—1Ti 6:14-16.

DECLARED RIGHTEOUS AND RAISED AS A SPIRIT BEING IN HEAVENS Adam was created by God as a man-flesh and was righteous, but he failed, he did not set a perfect example of godly devotion. Jesus was conceived by holy spirit born of a woman was also a man-flesh. (John 1:14New International Version (NIV)" The Word became flesh and made his dwelling among us. We have seen his glory, the glory of the one and only Son, who came from the Father, full of grace and truth." Jesus was righteous to the end and so He was resurrected as a spirit being in heavens.Thus, Jesus was “a corresponding ransom,” not for the redemption of the one sinner, Adam, but for the redemption of all mankind descended from Adam.

DEATH WILL BE NO MORE: Given the keys of Death and Hades:(Rev. 1:18 (NKJV) " I am He who lives, and was dead, and behold, I am alive forevermore. Amen. And I have the keys of Hades and of Death." And which he will cast into the (symboplic ) lake of fire( REV20:14) to be consumed that is to exist no more , meaning the second death. RAISE THE DEAD  : Granted powers to judge and raise the dead (John 5:21-30) John in verse 26 writes,  (NKJV) "For as the Father has life in Himself, so He has granted the Son to have life in Himself." John 5:28-29 REDEEMER OF MANKIND: Romans 5:12-19, 7:14-25 MAN MEDIATOR: (NIV) 1 Tim. 2:5-6 " For there is one God and one mediator between God and mankind, the man Christ Jesus, 6 who gave himself as a ransom for all people. This has now been witnessed to at the proper time."

In his book "TRUTH IN TRANSLATION: Accuracy and Bias in English Translations of the New Testament", Jason David BeDuhn, an associate professor of religious studies at Northern Arizona University, analizes ten major English translations (including KJV) of the Greek scriptures and writes that the only two correct renderings are by the NRSV and the NWT. He states, "There is no reason to think that the 'Holy Spirit' is involved in this passage. Was Christ justified in or by the Holy Spirit? The parallel that is drawn is 'in flesh' rules out such a reading".

NRSV "He was revealed in flesh, vindicated[b] in spirit,[c] seen by angels,proclaimed among Gentiles, believed in throughout the world taken up in glory."

NWT (New World Translation) "He was made manifest in flesh, was declared righteous in spirit, appeared to angels, was preached about among nations, was believed upon in the world, was received up in glory."

The word "Θεοs" does not appear in either WHNU or the Nestle Aland critical edition of the Greek Testament on which most English translations are based. Noted below. 

(NA) καὶ ὁμολογουμένως μέγα ἐστὶν τὸ τῆς εὐσεβείας μυστήριον· ὃς ἐφανερώθη ἐν σαρκί,ἐδικαιώθη ἐν πνεύματι, ὤφθη ἀγγέλοις, ἐκηρύχθη ἐν ἔθνεσιν, ἐπιστεύθη ἐν κόσμῳ, ἀνελήμφθη ἐν δόξῃ. (WHNU) και ομολογουμενως μεγα εστιν το της ευσεβειας μυστηριον ος εφανερωθη εν σαρκι εδικαιωθη εν πνευματι ωφθη αγγελοις εκηρυχθη εν εθνεσιν επιστευθη εν κοσμω ανελημφθη εν δοξη

There are many different translations and no two are alike, I have noticed it and so have you, and your alarmed. The KJV was based on The Textus Receptus by Erasmus and not based on the ancient Greek Manuscripts . At the time the KJV was written, knowledge of the Greek Koine was very limited, further older manuscripts have been found which made it necessary to revise the bibles. Bias and beliefs of the translators also is a reason for the differences.

BELOW IS AN EXPLANATION OF THE VERSE 1 TIMOTHY 3:16 BASED ON SCRIPTURES. So what does it mean " vindicated in spirit" and " manifest in the flesh"mean? And what are the benefits to mankind?

*MANIFEST IN THE FLESH Jesus, who was “the Word” of God, “out of heaven,” divested himself of spirit nature and “became flesh.” (1 Cor. 15:47; Phil. 2:5-8; John 1:14;) That in being born as a human he was no spirit and that he did not merely assume a fleshly body, as angels had done in the past (Gen. 18:1-3; 19:1; Jos. 5:13-15), is attested to by the apostle John, who says that one is antichrist who denies that Jesus Christ came “in the flesh.” (1John 4:2, 3) In order to provide the ransom for mankind and thereby to help those who would be his associates in the heavenly calling, the Word became flesh, being born all human, no incarnation. The Bible tells us this: “Since the ‘young children’ are sharers of blood and flesh, he also similarly partook of the same things.” (Heb. 2:14-16) His earthly sojourn was spoken of as “the days of his flesh.” (Heb 5:7) “The bread that I shall give is my flesh in behalf of the life of the world,” Jesus said. He went on to state that those hoping to remain in union with him must ‘eat his flesh and drink his blood.’ Not appreciating the spiritual, symbolic significance of his words, some construed the statement as cannibalistic and were shocked. —John 6:50-60.

VINDICATED IN SPIRIT God’s Son. God’s “only-begotten son,” the Word, was a spirit person like his Father, hence “existing in God’s form” (Php 2:5-8), but later “became flesh,” residing among mankind as the man Jesus. (John 1, 14) Completing his earthly course, he was “put to death in the flesh, but [was] made alive in the spirit.” (1 Tim 3:16, 1 Pet. 3:18) His Father resurrected him, granted his Son’s request to be glorified alongside the Father with the glory he had had in his prehuman state (John 17:4, 5), and God made him “a life-giving spirit.” (1 Cor. 15:45) The Son thus became again invisible to human sight, dwelling “in unapproachable light, whom not one of men has seen or can see.” —1 Tim. 6:14-16.

DECLARED RIGHTEOUS AND RAISED AS A SPIRIT BEING IN HEAVENS Adam was created by God as a man-flesh and was righteous, but he failed, he did not set a perfect example of godly devotion. Jesus was conceived by holy spirit born of a woman was also a man-flesh. (John 1:14 New International Version (NIV) "The Word became flesh and made his dwelling among us. We have seen his glory, the glory of the one and only Son, who came from the Father, full of grace and truth." Jesus was righteous to the end and so He was resurrected as a spirit being in the heavens. Thus, Jesus was “a corresponding ransom,” not for the redemption of the one sinner, Adam, but for the redemption of all mankind descended from Adam.

DEATH WILL BE NO MORE: Given the keys of Death and Hades:  (Rev. 1:18 (NKJV) " I am He who lives, and was dead, and behold, I am alive forevermore. Amen. And I have the keys of Hades and of Death." And which he will cast into the (symbolic) lake of fire  (Rev. 20:14) to be consumed that is to exist no more , meaning the second death. RAISE THE DEAD: Granted powers to judge and raise the dead (John 5:21-30) John in verse 26 writes, (NKJV) "For as the Father has life in Himself, so He has granted the Son to have life in Himself." John 5:28-29 REDEEMER OF MANKIND: Romans 5:12-19, 7:14-25 MAN MEDIATOR: (NIV) 1 Tim. 2:5-6 "For there is one God and one mediator between God and mankind, the man Christ Jesus, 6 who gave himself as a ransom for all people. This has now been witnessed to at the proper time."