I'm sorry, but Jesus DID NOT speak out against denominations. He spoke out about false teachings. There were no denominations to speak of in His day, and local Christian churches did not appear until after He left us with the Great Commission .
I feel just as comfortable in a Methodist or Pentacostal church as I do in a Baptist. Why? Because they all agree in Jesus as the Son of God, and that He is the only way to salvation. Their other differences are minor, and in no way interfere with God's work, except in those who will let it.

Now, James and Paul seemed to disagree on works and faith. At first glance you would think they were talking about two different things, but deeper study will help you realize they were speaking about the same thing, only in different ways from different angles.
If God is against denominations, then why do so many flourish? Surely ONLY ONE could have the TRUE message of God!
I don't think so. Reading the Bible, and then reading it and understanding it, are two entirely different things.

Do I have a better than average understanding of the Bible? While I by no means consider myself a Bible scholar, I do think that years of Bible study and Bible teaching have prepared me to have a better than average knowledge and understanding of God's Word.
At any rate, our efforts are to be directed at bringing the lost to Jesus, and leaving the confusion of the world's "church" out of our own.