Fighting doubt with the words of Christ
Jesus answered and said unto them, Go and shew John again those things which ye do hear and see. Mt. 11:4.
Here we have our Lord's answer to the doubts of John the Baptist (see Mt. 11:3). How did he receive assurance? He received assurance from the words of Christ. The same is true with us as well. At the end of the day, the only way all doubts can be silenced is through the word of God. A finite being by itself can never be completely sure they have arrived at infallible truth. The only way we can be sure is if we can be certain it is God who is speaking. This is why William Lane Craig differentiates between knowing the truth and showing the truth. We can show the truth through the arguments of apologetics and reason. And this can certainly play a part in our knowing the truth, but the only way we can really be sure that what we believe is true is through the witness of the Spirit in our hearts to God’s truth in Scripture. Assurance is obtained when we really meet God in the pages of the Bible.
Let us see how this works out in particular cases. First of all, how do we face doubt when we are doubting our relationship to Christ? To begin with, you don’t just listen to your feelings. Rather, you listen to God’s word. What does it say to you? If you are doubting your relationship with God because you feel the weight of sin upon your mind and heart, then you need to hear God’s word inviting you to confess and repent of your sin and to be cleansed afresh by the blood of Christ: “But if we walk in the light, as he is in the light, we have fellowship one with another, and the blood of Jesus Christ his Son cleanseth us from all sin” (1 Jn. 1:7).
You don’t need to fixate on your past, you need to look to Christ, for this is exactly what God’s word tells us to do. You shouldn’t remain in your sin, you need to follow Christ, for this is what God’s word tells us to do. And it tells us that when we do so, we will experience anew the fellowship of the Holy Trinity.
What if we are doubting God’s provision and care for us? Again, we need to listen carefully to the promises of God on our behalf. We don’t let our circumstances drown out the sweetness of God’s sure word. Here Abraham is an example to all of us: “Who against hope believed in hope, that he might become the father of many nations; according to that which was spoken, So shall thy seed be. And being not weak in faith, he considered not his own body now dead, when he was about an hundred years old, neither yet the deadness of Sarah’s womb: He staggered not at the promise of God through unbelief; but was strong in faith, giving glory to God; and being fully persuaded that, what he had promised, he was able also to perform” (Rom. 4:18-21).
What if we are doubting the very truthfulness of God’s word? Again, we need to listen to the word of God. G. Campbell Morgan, the predecessor to Martyn Lloyd-Jones at Westminster Chapel, early in his ministry faced a growing uncertainty in Scripture as he was confronted with the arguments of skeptics. The questions became greater and more unanswerable until he finally reached a crisis. As Morgan's daughter-in-law related in his biography:
"At last the crisis came when he admitted to himself his total lack of assurance that the Bible was the authoritative Word of God to man. He immediately cancelled all preaching engagements. Then, taking all his books, both those attacking and those defending the Bible, he put them all in a corner cupboard. Relating this afterwards, as he did many times in preaching, he told of turning the key in the lock of the door. 'I can hear the click of that lock now,' he used to say. He went out of the house, and down the street to a bookshop. He bought a new Bible and, returning to his room with it, he said to himself: 'I am no longer sure that this is what my father claims it to be—the Word of God. But of this I am sure. If it be the Word of God, and if I come to it with an unprejudiced and open mind, it will bring assurance to my soul of itself.'"
That is exactly what happened. “That Bible found me,” he said, and from that point on  he remained committed to the truthfulness of God’s word. Jonathan Edwards once said, “The gospel of the blessed God does not go abroad a begging for its evidence, so much as some think; it has its highest and most proper evidence in itself.”
At the end of the day, because the Bible is in fact the word of God, it is the source at which we should seek to quell all our doubts, answer all our questions, and silence all our fears.
This is from the Religious Affections, see http://www.leaderu.com/cyber/books/religaffect/rapt3sec05.html