I think the factory harness had a ground wire for the coil/regulator/relay support plate, but I thought it had an ring terminal. Looks like a spade in your photo.
The yellow wire goes to a capacitor to dampen alternator whine coming into your radio.
The odd stud on your starter relay is to bypass the ballast resistor and provide full voltage to the coil for stronger spark while cranking. Not sure if your MSD system accomodates that feature.
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