1. The PCV should be connected to its own manifold vacuum source (there's a fitting on the underside of the upper intake).
2. The 3 barb hookup? I'm not sure what you mean by this. If you got a parts store PCV, one of the ports remains capped, since most of them come with two ports for interchangability with other vehicles.
3. If you mean the connector that goes on the tube from the MAF to TB, the tube goes from there to the oil fill tube on the valvecover. Its purpose is to bring metered fresh air into the crankcase, so it can be expelled through the PCV.
4. You'll only need to make a hole in the passenger side valvecover for the oil fill tube.
5. See number 3. If you decide to run a breather, you need to eliminate the PCV system, or you'll be drawing in unmetered air and have one hell of a vacuum leak.
No, the pcv is on the back of the lower intake. What you are lookin at is the port for the vacuum coming from the tree.
If it's hitting the v/c, just take that fitting off and cap it off, that's what I did because I had the same problem.
FWIW, you really don't need to use all the ports on the intake. I just have one to the vacuum tree and one from the intake to the FPR, and that's it. I'm running not pcv.