I want to focus on Johns question. Ill leave others to answer in full .
John was asking about the end times . Specifically what advent they were in . He himself had unanswered questions . That is different than doubts.
Reasons as follows :
John The Baptists' mother Elizabeth , and Mary were cousins , making their mothers sisters. Making Jesus and John second cousins . John had grow up being taught who Christ was, recall his mothers statement made follows :
43 And whence is this to me, that the mother of my Lord should come to me?
44 For, lo, as soon as the voice of thy salutation sounded in mine ears, the babe leaped in my womb for joy.
45 And blessed is she that believed: for there shall be a performance of those things which were told her from the Lord.
46 And Mary said, My soul doth magnify the Lord,
47 And my spirit hath rejoiced in God my Saviour.
(They recognized the prophecy given to Abraham about the promised Messiah )
54 He hath helped his servant Israel, in remembrance of his mercy;
55 As he spake to our fathers, to Abraham, and to his seed for ever.
( They recognized the Messiah has come .
What they may or may not have fully realized is there would be a second advent .
Another thing to consider is the unrecorded years of Christ from age 12 to the beginning of Ministry. While they were only six months apart in age ; Its possible Christ and John were not together during this time ; leaving John with Not doubt ; but unanswered questions.
Again John was actually asking is this the end , or do we look for another advent ? We can know for certain this is what John was asking, because of the reply given .
Jesus's replied that He was fulfilling prophecy of Himself .
Specifically He was teaching Isaiah . The First advent had arrived . )
3 And said unto him, Art thou he that should come, or do we look for another?
4 Jesus answered and said unto them, Go and shew John again those things which ye do hear and see:
5 The blind receive their sight, and the lame walk, the lepers are cleansed, and the deaf hear, the dead are raised up, and the poor have the gospel preached to them.
Jesus was handed the book of Isaiah and taught the following :
Luke 4:14-21 kjv
14 And Jesus returned in the power of the Spirit into Galilee: and there went out a fame of him through all the region round about.
15 And he taught in their synagogues, being glorified of all.
16 And he came to Nazareth, where he had been brought up: and, as his custom was, he went into the synagogue on the sabbath day, and stood up for to read.
17 And there was delivered unto him the book of the prophet Esaias. And when he had opened the book, he found the place where it was written,
18 The Spirit of the Lord is upon me, because he hath anointed me to preach the gospel to the poor; he hath sent me to heal the brokenhearted, to preach deliverance to the captives, and recovering of sight to the blind, to set at liberty them that are bruised,
19 To preach the acceptable year of the Lord.
20 And he closed the book, and he gave it again to the minister, and sat down. And the eyes of all them that were in the synagogue were fastened on him.
21 And he began to say unto them, This day is this scripture fulfilled in your ears.
( Now if ; you go to Isaiah and continue reading, after the part He closed the book on, it'll lead into the second advent which had not happened during that time .) Because its yet future to even us today . .
Isaiah 61 kjv
1 The Spirit of the Lord God is upon me; because the Lord hath anointed me to preach good tidings unto the meek; he hath sent me to bind up the brokenhearted, to proclaim liberty to the captives, and the opening of the prison to them that are bound;
2 To proclaim the acceptable year of the Lord,
( At this part Christ closed Isaiah and said it is fulfilled. The part He did not read : ) .
"and the day of vengeance of our God; to comfort all that mourn;" .
A note on The Scribes and pharisees ; I'll mention in passing, these are no ordinary members of the synagogue.
John would say of them:
But when he saw many of the Pharisees and Sadducees come to his baptism, he said unto them, O generation of vipers, who hath warned you to flee from the wrath to come?
There is a running teaching through The Bible ; that can truly only be grasp when understood in its entirety ; that the priesthood became polluted many hundreds of years before Christ . Christ obviously knows who they are, and this was not lost to John how they misrepresent themselves to be something they're not .
These would be of those who Christ would say they claim to be Judah and are not and do lie etc. ; they sit in the seat of Moses, but are of their father The Devil . This group had no intention of listening to Christ, let alone John the baptist .