Ya, we also think God is present every where at the same time ..
AbdulKalam wrote: "Regarding 'begotten son' check Luke 3:38 'son of Enos, son of Seth, son of Adam, son of God.'. Here Adam is also son of God."
Read the entire section (Luke 3:23-38). Notice the first verse:" Now Jesus Himself began His ministry at about thirty years of age, being (as was supposed) the son of Joseph..."
Notice the parenthetical. Since Joseph was not Jesus' biological father (everyone thinking that He was, because Joseph did NOT shame Mary by pointing out that she was pregnant BEFORE they both had been brought to the marriage), someone else is the father. Mary, being a virgin (attested to by the midwives who delivered her), had experienced an immaculate (or virgin) birth for Jesus. Had the virgin birth been biological only, the child would be female. The DNA held by the female human being is two (2) "X" chromosomes in each cell of her body. In order for a male to be born, one of those "X" chromosomes has to be replaced with a "Y" chromosome. They are not self-generating. Joseph had not provided it. No other human being had provided it. That leaves only one alternative - God. Creation is uniquely the purview of God. [On the other hand, Satan is the destroyer - given measured release from God's bindings, when needed.]
That begs the question as to "how" God provided it. The Bible passages describing the "annunciation" (archangel Gabriel announcing God's selection of a Hebrew woman to bear the Son of God) state that the Holy Spirit (third person of the Trinity, the one who would inhabit each believer's heart) would "overshadow" her... Now, when God created the universe (Genesis 1), He "overshadowed" the waters. You can try to read into it any number of explanations which make sense to men. But, I think that, since God is not limited by human characteristics, we men shall not know what has not been explained - but those souls "returning to God" will understand, when everything is unveiled over eternity.
The lineage lays out a list, each human "begets" a "son" (not "Son"), in keeping with the Christian annotations for clarity distinction between mankind and God. Man was a creation (separate and non-existent prior to creation), not a portion of God (as the Son and Holy Spirit are, with the Father) who existed from eternity past. Let's not fall into the trap of trying to describe God in human limitations, as if they are specific independent persons... Let's use an example to clarify (presuming you are married male and have at least one child). AbdulKalam is simultaneously a father, a son, and a grandson. You are not three individuals, but three relationships defined by roles. As a father, you have one role (assigned certain specific characteristics). Similarly, as son and grandson, you have other distinct roles. Your roles overlap only in that you are one individual and those roles interact.
Examine Matthew 1:1-16. The phrasing used for Jesus' relationship to Joseph and Mary: " And Jacob begot Joseph the husband of Mary, of whom was born Jesus who is called Christ." Notice that Joseph is referred to as "the husband of Mary", and the attribution of birth attributed to Mary alone ("Mary, of whom was born Jesus..."). After all the painstaking soandso-begot-soandso (in so many words), why is Jesus not so listed? There is no "Joseph begot Jesus". Joseph is not Jesus' biological father, which this list represents between prior generations. As I pointed out, there is only one option for Father. The Father's substance was provided to Mary, in the form of the "Y" chromosome which made a boy possible. And God, Himself, inhabited Jesus (true man) as His Soul (true God)... Here is the catch - Mary's lineage is also through the "line of David". Whether He's referred to by his father's line or His mother's line, He's still a son of David - a royal line.
AbdulKalam wrote: "See Luke 1:31-32 ' And now, you will conceive in your womb and bear a son, and you will name him Jesus.  He will be great, and will be called the Son of the Most High, and the Lord God will give to him the throne of his ancestor David...' Did you notice 'he will be "called" the Son of Most High'? It means Son of God was only a name of Jesus."
I suggest looking at Matthew 1:23 (Immanuel = "God with us"). If you read the Bible through, you will notice something significant. God often calls men by names *other than* those supplied by the person's parents. We discussed the facets of God being "named" (which describe collected characteristics). God uses names this way - look at Jesus speaking to his first disciple Simon (renamed "Peter", and what "Peter" means). Look also at Revelation 19:11-16 - many names are attributed to the Son of God, seen now in power and glory.
AbdulKalam wrote: "'The only Son' as stated in John 3:16, is actually a misinterpretation. The original Bibles had 'the unique Son' in its place, which was replaced by the current words by Jerome in around 336 AD. [http://www.mostmerciful.com/gideon-bible.htm]
Your quotation is not NKJV John 3:16. The NKJV inserts "begotten" between "only" and "Son" in your quote. The website you provide is Islamic - and the credentials of the host are suspect as someone well educated in Christian studies. Would you expect a Jewish scholar to convincingly (and supportively) expound on the validity of Islam? I strongly expect your answer is, "no".
The following is attributed to: Robert Dean Luginbill, Ph.D; Classical and Modern Languages.
However, the ancient Greek referred to, "monogenes", is literally "one begotten" - and not translated as "unique". I found [www(dot)ichthys(dot)com(slash)mail-Only-Begotten-Mother-Of-God-On-This-Rock(dot)htm; question 1, response 1] which I think ties Hebrew and Greek together to resolve the uncertainty. For interest's sake, you might also read (question 7, response 7) further.