The black flap is the plastic radiator shroud. It's supposed to be up against the radiator tank. You should be able to flex it enough to get it around the A/C high pressure switch. It may require removing a few of the shroud bolts on that side.
Yes, the bolts should be shorter so that the threads are flush to the top side of the nut when tight.
You have the light weight hi-torque starter. The original starter had an extra wire coming out of the starter solenoid, it provided power the the ignition resistor by-pass circuit. The new upgraded starter does not have this extra lead. The factory engine harness used a single pin bullet connector that plugged into the OEM starter wire. Some folks will cut the end of the engine harness wire and replace it with a ring terminal. Then attach it to the starter with the small W/R wire at the solenoid. I prefer not to cut the harness connector off, but rather make a short 5 inch harness with a ring terminal on one end and male bullet connector on the other. Install the small lead with the W/R wire and plug the other end into the factory harness connector. The important thing is to get rid of the blue scotch lock wire tap. You will need to put some heat shrink over the spot on the W/R wire where the tap cut into the insulation.
Dennis