Here is a great list of how to pray for your church:
9 Ways to Pray for Churches and Pastors
Found in the 9Marks 2013 report:
1. Expositional Preaching: pray that more pastors will commit to preaching the whole counsel of God, making the point of the passage the point of their sermons.
2. Biblical Theology: pray that more pastors will preach about the big God from the big Story of the Bible, protecting the church from false teaching.
3. The Gospel: pray that pastors will faithfully proclaim the gospel every chance they have. Pray their churches will ask for nothing more than the good news of salvation through Jesus Christ.
4. Conversion: pray that more churches would grasp the doctrine of conversion rightly, and shape their practices to promote born-again believers, not nominal believers.
5. Evangelism: pray that churches will be bold and faithful in proclaiming the Good News of Jesus.
6. Church Membership: pray that churches will take the biblical call to church membership seriously, and encourage the whole body of Christ toward holiness and active participation.
7. Church Discipline: pray that churches will grow in purity and holiness as they seek to warn, rebuke, and admonish lost sheep.
8. Discipleship and Growth: pray that Christians will grow in their knowledge of the Word, and their commitment to discipling one another.
9. Biblical Leadership: pray that God will raise up many faithful shepherds to guard, teach, and encourage his flock.
(I found this at the gospel coalition website on Justin Taylor’s blog)