Question:When speaking to an atheist, what Scripture is most useful to challenge one to understand that God does exist? And how can I convince him that this God is merciful, if he has lived life in a body wrecked by pain?
You are starting off on the wrong foot since an atheist does not accept the Bible as being God's word. It is not a simple matter of turning to some passage which he cannot explain and therefore comes to the conclusion that God must exist.
As I explained in "How do I convince an atheist to believe in the Bible?" you must approach an atheist as a long term project. You need to find some common ground where both of you agree and work from there. Small points to show that the Bible is sensible will go further than long, complex arguments. See "How do I reach out to my atheist roommate?" for a discussion of this.
Are you saying that this person blames God for his pain? Or are you saying that a major road block to his accepting God is the fact that he is in pain? The former means he isn't a true atheist because to blame God is to acknowledge His existence. If it is the later, points about where suffering comes from and how those against God bring it into the world will make some inroads. The sermon "Does God Make the Handicapped?" might give you some ideas for starting points.