1. Since the Holy Spirit begot Jesus through Mary, doesn't that mean He has to be God the
Father of Jesus?
When the Bible uses "beget, begotten" specifically in the context of Jesus, it's referring to a metaphorical meaning and certainly not a literal meaning. It's never used in the context of the birth of Jesus. Also, it's important to note that the Bible does not teach that Mary and God the Father had any type of sexual relations whatsoever. The Father is indeed the Father of Jesus in terms of order, but not in terms of parenting Jesus.
2. When we call God a "He," who are we referring to? Is there are fourth person suggested by this?
For example, what if I say "I believe in God - I believe in Him." Who is the "Him" referring to? One or all of the persons of God, or the being of God?
Usually, the Trinity model has "God" in the middle, and the Father, Son, and Holy Spirit in a Triangle around it. However, when we call God a "He," this is what it seems to suggest instead:
{-----------Son (person)
GOD (person?){ ------------Father (person)
{---------- Holy Spirit (person)
Or does it not?
In Deuteronomy 6:4 it says "Hear O'Israel the Lord is our God, the Lord is one". So this is the ultimate proclamation of God's oneness and unity. For example, You can say there is "one nation" or "one team". God in His being is one, but that doesn't mean that God is one person. The word for "one" in Deuteronomy 6:4 is the Hebrew word "echad", as some Chassidic Jewish Rabbis have put it, based on the teachings of the Lubavitcher Rebbe "Echad, on the other hand, represents the fusion of diverse elements into an harmonious whole. The oneness of echad is not undermined by plurality; indeed, it employs plurality as the ingredients of unity." (Reference: Chabad.org) So, saying God is one does not exclude the idea of God being more than one Person, it just says that He is one being, in the sense of unity. As to when you call God singular pronouns, that's how we should speak about God. He is one, when I speak of "He" or "Him" I am speaking about the one only true God who is triune in nature.
3. When in Isaiah 53 God says that He will raise up His servant...who was speaking? Is the Father speaking now? Is the Son speaking about His servant (Himself?)?
In this context, I think we can agree it is the Father speaking and the Son being sent. However, the Father and Son are always in perfect agreement. We learn from the carmen christi, Philippians 2:5-11 that the Son who was in the form of God and equal with God (the Father) humbled Himself and came down in the form of a servant, even to the point of death on the cross.
4. If Jesus has the nature of God, how can He be "granted" to have life in Himself?
I recommend looking at Philippians 2:5-11 and studying it out. It speaks about Jesus who was equal with and in the form/nature of God and humbling Himself. The word "humble", "kenosis" in Greek means to empty ones self. So Jesus literally emptied Himself of all Godly attributes and was fully relying on the Father. As you notice that Jesus never performed a miracle until He was baptized with the Holy Spirit. John 17:5 speaks of the glory that Jesus shared with the Father before the world was. Jesus was praying to the Father to glorify Him with that glory which He had. (all the divine attributes He emptied Himself of).
5. If Jesus has the nature of God, why would He say "Not my will but yours be done?" Isn't His will God's will, since He is God incarnate? (not the Father but the Son.)
Just for clarification the usage of "God" in the New Testament primarily refers to the Father and "Lord" primarily refers to Jesus. There are many reasons why Jesus could have done this.. One reason could be that Jesus was teaching us something here that even if we don't want to do things that we must be humble and rather do what God wants. Sort of like a lesson for us rather than something Jesus was actually. Remember Jesus said "For I have come down from heaven, not to do My own will, but the will of Him who sent Me." in John 6:38. So, you can simply read it just as it says.. That Jesus is not necessarily in disagreement with the Father but it shows the perfect harmony and love that they share. They don't have two separate interests or desires, Jesus is showing His unity with the Father to accomplish His perfect will. There are a number of other ways to interpret it, but I believe either of these interpretations could show that Jesus was not denying to be God in any sense.
6. If Jesus has the nature of God, why would He say "If you believe in Me, you do not believe in Me, but in Him who sent me?" How can you not believe in Jesus if He is God?
Jesus came to be a servant and glorify the Father. Going back to John 17 Jesus speaks about glorying the Father and how He did not receive His own glory on earth. Jesus glorifies the Father, the Father glorifies the Son and the Holy Spirit glorifies Jesus, as we learn from John 16.
7. A more obvious question, why did the Son not know the day of His return? I know the argument that He laid aside divine rights when He took on human flesh - but how can you lay aside knowledge? I understand laying aside authority (which was given back to Him I guess when He came here...and when He went into heaven), but knowledge?
I wouldn't question God by asking "how" He could do something as if there are limitations as to what God can and cannot do. I would agree with that explanation that Jesus emptied Himself of His knowledge and divine attributes and that's why He did not know the hour. For a very detailed answer and a lot more information on the subject I would highly recommend looking at this article; The Lord Jesus: The Divine Son who is Superior to all Creation
8. Can I say "There is one God, the Father," as in 1 Corinthians 8:6, or must I say "There is one God, the Father, Son, and Holy Spirit?" Wasn't Paul excluding the Son and the Holy Spirit here?
I understand we could say "The Father is the one God." But can we say "the one God is the Father..."?
"Yet for us there is but one God, the Father, from whom are all things and we exist for Him; and one Lord, Jesus Christ, by whom are all things, and we exist through Him." 1 Corinthians 8:6.. I think it's very important to not leave out "and one Lord Jesus Christ by whom are ALL things, and WE exist through Him".. A lot of scholars believe this is Paul's version of Deuteronomy 6:4 (called the Shema), One God and One Lord. God the Father and Lord Jesus. "Hear Israel, the Lord our God, the Lord is one" (Deuteronomy 6:4).. It is true that the Father is the only true God (as John 17:3 says).. However, it's also true Jesus is the only true God and the Holy Spirit is the only true God. Father, Son and Holy Spirit = 1 true God. You can also say that they are equally all the one true God.
There are more questions I have, but this is suitable for now. Please understand - I really am trying to get a hold on this. Why is it so complicated? I have read
much on the Trinity. I've listened to James White's debates, I've read
Putting Jesus in His Place, I have tried to study the passages of Scripture with the little knowledge I have, I have done more - but just as the Trinity seems to be right, another question pops up in my head (and it usually goes unanswered).
Just try to answer the best you can - but please do it after praying and searching deeply. I don't want throw-off answers - this is serious. Don't even look at my age, just look at the questions.
Grace and Love