The following articles written over at Expository Thoughts (as well as the comment threads) are excellent posts (and responses) dealing with the difficulties that inevitably arise when studying the Bible. I commend them to your careful reading.

An Introduction

Christological Hermeneutic

Apostolic Hermeneutic

The NT View of the OT

The Priority of the Old Testament

Common Mistakes in Preaching

Walt Kaiser on 1 Peter 1:10-12

Paul’s Use of Hosea in Romans 9:25-26

Concluding Thoughts