If the Holy Spirit is God, and God can not be in the presence of sin, then how can the Holy Spirit dwell in me a sinner? If we believe in the Trinity, in essense that the Holy Spirit is God, and we believe that God can not be in the presence of sin, then how can the Holy Spirit dwell within me a sinner?
The idea that God cannot be in the presence of sin may come from the prayer in Habakkuk 1:13.  In the NIV it says, "Your eyes are too pure to look upon evil."  

The question, then, is, "Is this teaching the God is unable to look at evil?"  If it is teaching that, then this would need to fit with the whole of Scripture.

Psalm 139 expressly states that God knows and sees everything that occurs, which would include evil.  God also came to Adam and Eve after their sin.  He visited Sodom to see the evil that was there.  He observed the Israelites fashioning a golden calf and worshiping it.  In Job, Satan comes into God's presence and has discussions with Him.  Jesus, too, walked among us and certainly was in the presence of evil His whole life.

So, it seems clear that God does see evil and He does allow sin to come into His presence.  Indeed, if all have sinned (and continue to do so), God must be able to be in the presence of sin to indwell those who have placed their trust in the redemption of Christ.

A key point here is that those who have trusted Christ are, according to the Scriptures, declared righteous in His sight--forgiven.  The debt is fully paid.  No charge can be entertained against us.  

Now God's work of redemption will be fully complete when He fully removed that which He hates (sin) from that which He loves (His people).