2 Timothy 3:16 doesn't leave room for picking and choosing - "ALL scripture is God breathed and is useful for teaching, rebuking, correcting and training in righteousness..." You have to read it all in the light of the central theme of God revealing himself through Jesus, and Jesus' death for our salvation, which means you don't take some stuff literally (such as OT commands that applied to Israel and were part of specific covenants that we on this side of the cross are not under) but there are practical words and exhortations that need to be taken at face value.
Regarding content written "specifically for churches", I think that Paul's words and advice can appropriately be applied to us in our churches. An example I'd cite are the letters to the seven churches in Revelation - even though specific churches are named, the number 7 is symbolic of the entire group of believers, and thus should not be restricted to the people who were in the 7 churches addressed. The truth is that the issues facing the early NT churches are very similar to issues being faced in the churches of today, and God has spoken through Paul and the other NT authors so we would do best to consider their words and how they relate to us today