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The PCV valve and hose are connected to the filter piece that is supposed to be inside the air cleaner. The purpose of the PCV valve is to allow positive pressure in the engine sump to escape [into the intake to be burned]. Bubba new enough that he left the PCV system connected, but just allowed the discharge to go into the air. No big deal for the car/engine; not the right thing for emissions control. You can leave it as-is or you can find an air cleaner with the intake nipple on the housing so that you can connect it up. The other stuff is "minor"...you shouldn't need a new wiring harness for that. You SHOULD purchase an Assembly Instruction Manual (AIM) so you can see how all that "stuff" is hooked up on your vehicle.
That is the crankcase vent filter. When PCV valve draws dirty air out, it lets clean air in. It is normally mounted inside factory air cleaner assembly.
That threaded hole is normal. For a bracket you dont have or someone left off.
If you are asking about that plastic covering on the wires? You can buy it new.
Welcome to the forum Zeed. She do look good from the outside. Those few things under the hood are minor. The PCV, unless you get it venting back in the intake/breather somehow, you may get a little hot oily smell inside the cabin. East fix though.
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