Not sure what this black plug is supposed to plug into? The green wire has been cut, and there's a green wire coming out of the wire loom below the ballast that's been cut, should those two ends be connected? Also what does the smaller plug below it with the brown and grey wire hook to?
The smaller plug connects to the main engine harness that attaches to the ps valve cover. It's the same style of connector that attaches to the distributor so it's probably for that.
Lastly, this small plug is over by the bulkhead and is unplugged as well. What is it for and where should it plug into?
That one doesn't connect to anything. It's not connected on my car either. It might have been a test port to test the harness at the factory.
I attached the black wire from the pertronix to the -side of the coil, just not sure where to attach the red wire to. Also what is the little round thing below the Dist? The wire from it is attached to the + side of the coil.
Do the Pertronix instructions say to attach the red wire to a "keyed" ignition source? If so, you need to connect it to a dark blue wire. The blue wire has power in the "run" position only. The canister attached to the coil is a condenser used to reduce interference in the radio.
What do these two plugs hook to. This one plug is where the other end of the blue wire goes to, and it looks like someone spliced the two brown wires into the black wire? Not sure what to do about that? There is also a blue wire going to the other white plug but it comes out of the wiring loom.
The white plug goes to one side of the ballast resistor. Originally your car came with a 4 prong ballast. You have a 2 prong ballast installed now. The 4 prong ballast uses that special plug with the plastic pin on it so the wires can't be installed backwards.
I've got my original engine harness. It might be useful for me to just take pictures of it so you can see what it should look like and how all the wires connect.