Thank you for sharing your concerns. We will examine as many of these scriptures as we can in this limited space, and offer you other resources to help.
One of the first principles of understanding the Bible is that doctrine should be based on the whole Word of God and not just a few passages taken in isolation. The Bible itself tells us that "man shall not live by bread alone; but man lives by every word that proceeds from the mouth of the Lord " (Deuteronomy 8:3 Deuteronomy 8:3And he humbled you, and suffered you to hunger, and fed you with manna, which you knew not, neither did your fathers know; that he might make you know that man does not live by bread only, but by every word that proceeds out of the mouth of the LORD does man live.
American King James Version×, emphasis added throughout). Jesus Christ clearly endorsed this overriding truth by quoting these very words in rejecting Satan's distortion of Scripture (Matthew 4:4 Matthew 4:4But he answered and said, It is written, Man shall not live by bread alone, but by every word that proceeds out of the mouth of God.
American King James Version×; Luke 4:4 Luke 4:4And Jesus answered him, saying, It is written, That man shall not live by bread alone, but by every word of God.
American King James Version×).
The apostle Paul told Timothy that he should be "handling accurately the word of truth" (2 Timothy 2:15 2 Timothy 2:15Study to show yourself approved to God, a workman that needs not to be ashamed, rightly dividing the word of truth.
American King James Version×, New American Standard Bible). Singling out a few passages here and there is not a sound method of determining doctrinal truths. We must put together all the relevant scriptures on a particular subject to gain full understanding. Baptism is a case in point.
You stated that "baptism is not mandatory for salvation." Yet the early chapters of all four Gospel accounts refer to John the Baptist baptizing many people, including Jesus Christ Himself. John initially protested that he was not worthy to baptize Jesus, but Christ insisted. He wanted to set us an example that we all should follow.
And in fact, "Jesus made and baptized more disciples than John (though Jesus Himself did not baptize, but His disciples)" (John 4:1-2 John 4:1-2  When therefore the LORD knew how the Pharisees had heard that Jesus made and baptized more disciples than John,
 (Though Jesus himself baptized not, but his disciples,)
American King James Version×)—just as His followers do today. Jesus Himself said, "He who believes and is baptized will be saved" (Mark 16:16 Mark 16:16He that believes and is baptized shall be saved; but he that believes not shall be damned.
American King James Version×).
In his inspired sermon on the Day of Pentecost, when the Church was founded, the apostle Peter set out the proper order of events when he said, "Repent, and let every one of you be baptized in the name of Jesus Christ for the remission of sins; and you shall receive the gift of the Holy Spirit" (Acts 2:38 Acts 2:38Then Peter said to them, Repent, and be baptized every one of you in the name of Jesus Christ for the remission of sins, and you shall receive the gift of the Holy Ghost.
American King James Version×).Note that we should first repent, then be baptized, and then God responds to our obedience by giving us His Holy Spirit (Acts 5:32 Acts 5:32And we are his witnesses of these things; and so is also the Holy Ghost, whom God has given to them that obey him.
American King James Version×).
Even when God chose to reverse the normal order to miraculously demonstrate that He was calling gentiles to be part of His Church, Peter immediately said: "Can anyone forbid water, that these should not be baptized who have received the Holy Spirit just as we have?" Then Peter "commanded them to be baptized in the name of the Lord" (Acts 10:47-48 Acts 10:47-48  Can any man forbid water, that these should not be baptized, which have received the Holy Ghost as well as we?
 And he commanded them to be baptized in the name of the Lord. Then prayed they him to tarry certain days.
American King James Version×). We have no authority from God to omit water baptism from the salvation process. The apostles of Christ mandated it.
It is certainly true, as you have stated, that "the blood of Jesus washes away our sins." Yet we must also remember what Ananias (a man chosen by God to instruct Saul) said: "And now why are you waiting? Arise and be baptized and wash away your sins, calling on the name of the Lord" (Acts 22:16 Acts 22:16And now why tarry you? arise, and be baptized, and wash away your sins, calling on the name of the Lord.
American King James Version×). Water baptism symbolically washes away our sins, defined in the Bible as the transgressions of God's
Concerning the necessity of the laying on of hands, the apostle Paul told Timothy to "stir up the gift of God [the Holy Spirit] which is in you through the laying on of my hands"(2 Timothy 1:6-7 2 Timothy 1:6-7  Why I put you in remembrance that you stir up the gift of God, which is in you by the putting on of my hands.
 For God has not given us the spirit of fear; but of power, and of love, and of a sound mind.
American King James Version×). This is how one receives God's Spirit (Acts 8:17-19 Acts 8:17-19  Then laid they their hands on them, and they received the Holy Ghost.  And when Simon saw that through laying on of the apostles' hands the Holy Ghost was given, he offered them money,  Saying, Give me also this power, that on whomsoever I lay hands, he may receive the Holy Ghost.
American King James Version×; 9:17; 19:6).
As to the passage on the thief on the cross, it has been badly misinterpreted. You stated that "we can safely say that the thief went to heaven." But like all who have died except Christ, this man is not conscious in heaven but is awaiting the resurrection. Let's take another look at this passage.
One key to understanding its true meaning is the thief's request that Christ remember him "when You come into Your kingdom" (Luke 23:42 Luke 23:42And he said to Jesus, Lord, remember me when you come into your kingdom.
American King James Version×). Jesus comes into His Kingdom at the time of the resurrection, when the saints of God join Him on earth to rule with Him (see Revelation 5:10 Revelation 5:10And have made us to our God kings and priests: and we shall reign on the earth.
American King James Version×; 20:1-4). These events are yet future.
We should also ask ourselves, where exactly did Jesus go after He died? Did He go to heaven that same day? No, the Scriptures are quite clear that He went to the grave until His resurrection three days and three nights later, just as He said would happen (Matthew 12:40 Matthew 12:40For as Jonas was three days and three nights in the whale's belly; so shall the Son of man be three days and three nights in the heart of the earth.
American King James Version×; Acts 2:31-33 Acts 2:31-33  He seeing this before spoke of the resurrection of Christ, that his soul was not left in hell, neither his flesh did see corruption.  This Jesus has God raised up, whereof we all are witnesses.  Therefore being by the right hand of God exalted, and having received of the Father the promise of the Holy Ghost, he has shed forth this, which you now see and hear.
American King James Version×; 13:29-30, 34-35). So the thief could not have gone to heaven with Him that day. Jesus Himself didn't go to heaven that day!
Odd as it may sound to most people, heaven is not the reward of the saved. Scripture tells us that "no one has ascended into heaven but He who came down from heaven, that is, the Son of Man . . ." (John 3:13 John 3:13And no man has ascended up to heaven, but he that came down from heaven, even the Son of man which is in heaven.
American King James Version×; see also Matthew 5:5 Matthew 5:5Blessed are the meek: for they shall inherit the earth.
American King James Version×).
Importantly, the thief, though not yet baptized and converted, is not condemned without hope for salvation. He will be resurrected at the time of Christ's Kingdom and given the opportunity to be saved. For a much more detailed understanding of the incident with the thief on the cross, see pages 38 and 39 of our free booklet Heaven and Hell: What Does the Bible Really Teach? This publication explains why we neither go to heaven nor descend to hell when we die. The Bible consistently pictures death as a sleep from which we awake at the resurrection.
As for your reference to 1 John 1:9 1 John 1:9If we confess our sins, he is faithful and just to forgive us our sins, and to cleanse us from all unrighteousness.
American King James Version×, we must first realize that this verse, like the entire epistle of 1 John, is addressed to true Christians who have already repented, been baptized and received God's Spirit. When the New Testament uses the pronoun "we," it nearly always refers to Christians. Even righteous men and women of God slip and fall occasionally, and the apostle John is telling them—and us—what to do when this occurs.
Certainly our human minds are all too prone to come up with reasons why we might think it isn't necessary to obey God on a particular point (see Romans 8:7 Romans 8:7Because the carnal mind is enmity against God: for it is not subject to the law of God, neither indeed can be.
American King James Version×; Jeremiah 17:9 Jeremiah 17:9The heart is deceitful above all things, and desperately wicked: who can know it?
American King James Version×). But humble submission to God's Word and will is required of all who want to remain in His grace and to be saved in the end.
The free booklets The Road to Eternal Life and Transforming Your Life: The Process of Conversion explain water baptism in greater detail and why it is an essential step in the salvation process. You can request or download these free publications at www.gnmagazine.org/booklets. It requires a good deal of prayer, time and patient Bible study to correctly understand the biblical teachings of God.