There are some wires covered in flex loom, do they actually run between the power steering pump bracket and the head? or do they somehow run outside of it. Could you tell me which valve cover bolts use the bolts with the pin on it for the spark plug wire connectors?
Yes that wiring harness goes between the power steering pump and the head. There should be just enough room to tuck it up against the power steering pump and bracket, to keep it away from the head and header.
As for the studs, only the outside ones have studs, none of the inside. Here's the pattern as you're looking at the motor from the front of the car.