Doing as you suggested yielded this list (some explanations are mine and a few are directly from the website)...
1. God dwells in light (1 Timothy 6:16)/ God dwells in darkness, (1 Kings 8:12)
I dwell in the darkness. I dwell in the light—hmm, maybe that’s a conflict for me too!
God is omnipresent... we believe He is all places at once. Let's look at the quote from Timothy in context (I'm using NIV)...
1 Timothy 6:5 God, the blessed and only Ruler, the King of kings and Lord of lords, 16 who alone is immortal and who lives in unapproachable light, whom no one has seen or can see.
It's a description of Heaven and God on His throne not a statement of absolute dwelling. Let's look at the competing scripture...
1 Kings 8:10 When the priests withdrew from the Holy Place, the cloud filled the temple of the LORD . 11 And the priests could not perform their service because of the cloud, for the glory of the LORD filled his temple. 12 Then Solomon said, "The LORD has said that he would dwell in a dark cloud; 13 I have indeed built a magnificent temple for you, a place for you to dwell forever."
You would be better to call this one verse contradictory than the two in question. In context, though, Solomon is dedicating the Temple of God and God has come there to dwell in a dark cloud... His physical presence. Poor Solomon, as a man he doesn't know the future and the eventual destruction of the Temple. God didn't promise to dwell in this Temple forever, Solomon just invited Him to. This doesn't mean God isn't still omnipresent and there in the light and darkness in cave and in the valley... He's God. In both cases above, God on His throne in unapproachable light and in the darkness of the cloud, He is concealed from view. This isn't a contradiction.
2. Blasphemy against the Holy Ghost is unforgivable (Mark 3:29,Matthew 12:31)/ Believers are justified in all things. (Acts 13:39)
This is a definition thing, perhaps: Believers do not Blaspheme the Holy Spirit as they have accepted Jesus as God. The Pharisees were arguing the power of the Holy Spirit was the power of the Devil. Even so, Acts contrasts justification under the Law with justification of the Spirit. It may not be an absolute, just a comparison. Jesus, who would be the authority if the Bible is true, says All things will be forgiven accept for blasphemy of the Holy Spirit. Paul doesn't mention this one sin in his context of talking about Law vs. Grace! Do the proponents of this inconsistency qualify their own statements that concern a vast majority of the cases with exceptions for special cases? When they mention rain in any context do they make sure that they specify water rain and not frogs or walnuts or apples? I doubt it. (All rains are historically recorded.)
Again, the context is Law and Grace. My take is that Paul says that grace justifies believers from everything that cannot be justified under the Law. Blasphemy of the Holy Spirit was introduced with Jesus, therefore, not a part of traditional law.
3. John the Baptist is Elias (Matthew 11:14) /John the Baptist isn’t Elias (John 1:21)
To some degree, this is a case of he said, He said, but on a more interesting note...
In Matthew 11:14, Jesus says “And if you are willing to believe it, [John the Baptist] is Elijah who has come.” (NIV) The answer in John, is given by John, who the Bible never claims to be infallible. As far as John knows, he is not Elijah. He doesn’t feel like Elijah... He just thinks that he is the Voice in the Wilderness. He doesn’t necessarily know that God had meant him to the Elijah of the current age. There are NO contradictions between what God says on a metaphorical level, and John says on a personal level.
4. A brother will marry his brother’s widow (Deuteronomy 25:5) / Such a thing is unclean (Leviticus 20:21)
Here is a good place for context. Leviticus says marrying your brother’s wife is wrong, Leviticus 20:19 says to not have sex with your sister (apparently there’s room in there for sex with your brother, though...). Leviticus 20:20 says don’t have sex with your aunt, then Leviticus says don’t marry your brother’s wife, I would take this to mean that you shouldn’t marry your living brother’s wife. I think there’s room for this argument. Let's look at them in context...
Deuteronomy 25:5 If brothers are living together and one of them dies without a son, his widow must not marry outside the family. Her husband's brother shall take her and marry her and fulfill the duty of a brother-in-law to her. 6 The first son she bears shall carry on the name of the dead brother so that his name will not be blotted out from Israel.
Leviticus 20:21 "If a man marries his brother's wife, it is an act of impurity; he has dishonored his brother. They will be childless."
The first is very specific that the marriage takes place due to the DEATH of the brother. The second says that one brother is trying to marry the wife of his brother... dishonoring him. There is a big difference.
5. I came not to send peace, but a sword. (Matthew 10:34 / ... all they that take the sword shall perish with the sword. (Matthew 26:52, Revelations 13:10)
Jesus is speaking metaphorically... Let's look at it in context...
Matthew 10:34 "Do not suppose that I have come to bring peace to the earth. I did not come to bring peace, but a sword. 35 For I have come to turn
" 'a man against his father,
a daughter against her mother,
a daughter-in-law against her mother-in-law--
36 a man's enemies will be the members of his own household.'
37 "Anyone who loves his father or mother more than me is not worthy of me; anyone who loves his son or daughter more than me is not worthy of me; 38 and anyone who does not take his cross and follow me is not worthy of me. 39 Whoever finds his life will lose it, and whoever loses his life for my sake will find it.
Belief in Jesus brings division, even within a home. Jesus said as much. You can see the evidence here on Freerepublic. The second verse above is truly about swords... these verses don't contradict each other--really, they have nothing to do with each other, in context.
6. For wrath killeth the foolish man... (Job 5:2) / ... let not the sun go down on your wrath. (Ephesians 4:26)
Does the bible say how long it takes wrath to kill you? Job gives no indication that it is overnight. Therefore, quite easily they to not conflict. These are complementary, not contradictory. A reason not to let the sun go down on your anger is that it kills you over a period of time. Sources other than the Bible confirm this, I think they would condone the practice of limiting your anger to a calendar day. I think they would condone the Bibles other statements on anger too, like being slow to become angry.
In addition it says “wrath killeth a foolish man...” The possibilty exists that if you are not foolish, your anger won’t kill you. Is this not reasonable? In addition, one is a Hebrew word and the other is a Greek word in the original text. The Hebrew (ka’ac) word can also be used for spite, while the Greek form (parorgismos) can mean indignation or exasperation. Quite a difference between the two, isn’t there?
7. And no man hath ascended up to heaven.... (John 3:13) / ...and Elijah went up by a whirlwind into heaven. 2 (Kings 2:11)
Here, at last, is a good challenge. Let's look at the context on each, though...
John 3:10 "You are Israel's teacher," said Jesus, "and do you not understand these things? 11 I tell you the truth, we speak of what we know, and we testify to what we have seen, but still you people do not accept our testimony. 12 I have spoken to you of earthly things and you do not believe; how then will you believe if I speak of heavenly things? 13 No one has ever gone into heaven except the one who came from heaven--the Son of Man.
Jesus is clearly speaking of His teaching authority. He is castigating the teachers for not believing His teaching when He is speaking as a witness to what He knows. The context isn't that no one has ever gone up to Heaven. The context is that no one has come to Earth to testify to what they have seen there except for the Son of Man.
8. If I bear witness of myself, my witness is not true. (John 5:31) / I am one that bear witness of myself... (John 8:18)
John 8:18 continues “...my other witness is the Father, who sent me.” (NIV) In both cases Jesus invokes the idea of testimony of two witnesses being valid, in both Jesus offers another witness. Also the first sentence does not make sense read in this way. My testimony to myself is characteristically untrue if I say it. Apparently, if the list’s compiler says that he’s read the Bible it may become untrue just because he says it. The NIV reads true as valid.
This would synch with John 8:17, which reads “In your own Law it is written that the testimony of two men is valid” (NIV). In this case, it is obvious that if the testimony of two is valid, that Jesus may be saying that the testimony of one is not, by itself, valid.
9. A good man leaveth an inheritance to his children’s children... (Proverbs 13:22) / Sell that ye have... (Luke 12:33, Matthew 19:21)/ Set your affection on things above, not on things on the earth (Colossians 3:2)
This is another place where context is important...
Proverbs 13:20 He who walks with the wise grows wise,
but a companion of fools suffers harm.
21 Misfortune pursues the sinner,
but prosperity is the reward of the righteous.
22 A good man leaves an inheritance for his children's children,
but a sinner's wealth is stored up for the righteous.
23 A poor man's field may produce abundant food,
but injustice sweeps it away.
The context isn't that a good man has a DUTY to leave an inheritance for his children's children, just that he does. The inheritance is wisdom and God's favor. See the near verses to see the discussion... Proverbs does have a flow. The discussion is regarding the benefits of wisdom and the folly of sin. While the good man's heritage is good for generations, the sinner's will eventually pass to the good; "...but a sinner's wealth is stored up for the righteous."
10. And the priest shall burn all on the altar to be a burnt sacrifice, an offering made by fire, of a sweet savor unto the Lord. (Leviticus 1:9) / Your burnt offering are not acceptable, nor your sacrifices sweet unto me. (Jeremiah 6:20)
Jeremiah, throughout, refers to the present generation of Israelites. God is saying that even though he has asked for burnt offerings, “Your sacrifices are not acceptable.” Even the Old Testament suggests that sacrifice is not all God wants. Normally, gifts are a sign of gratitude and are almost always acceptable. But if your children come at Christmas times with fancy gifts, even though you know in your heart they are waiting for you to die, the gift doesn’t do much, does it?
11. Ye shall afflict your souls and offer an offering made by fire unto the Lord. (Leviticus 23:27) / For I spake not unto your fathers, nor commanded them in the day that I brought them out of the land of Egypt, concerning burnt offering or sacrifices. (Jeremiah 7:22)
Context...
Jeremiah 7:21 " 'This is what the LORD Almighty, the God of Israel, says: Go ahead, add your burnt offerings to your other sacrifices and eat the meat yourselves! 22 For when I brought your forefathers out of Egypt and spoke to them, I did not just give them commands about burnt offerings and sacrifices, 23 but I gave them this command: Obey me, and I will be your God and you will be my people. Walk in all the ways I command you, that it may go well with you. 24 But they did not listen or pay attention; instead, they followed the stubborn inclinations of their evil hearts. They went backward and not forward.
Context is important. The Bible isn't a list of do's and don't, it's a story of God and His people. He raises them from infancy with words and actions of "Thou shalt not..." and brings them to adolescence and maturity in His Son. In this seeming inconsistency of the Bible, we see a Father upset with His children. He didn't want burnt offerings because He likes the smell of smoke, he commanded burnt offerings as a sign of obedience. Jeremiah rails here and elsewhere against the current generation of Jews for turning their backs on their convenant.
This applies to #10 as well.
This took quite a while to answer. I sincerely hope you will read it in the spirit of knowledge it was written. If there are other challenges I haven't addressed, I will gladly discuss them with you.